http://amos.sourceforge.net/wiki/api.php?action=feedcontributions&feedformat=atom&user=DdsommerAMOS WIKI - User contributions [en]2026-04-30T05:54:02ZUser contributionsMediaWiki 1.23.5http://amos.sourceforge.net/wiki/index.php/AMOSAMOS2014-10-16T01:52:19Z<p>Ddsommer: </p>
<hr />
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<br />
The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.<br />
<br />
<br />
Quick links:<br />
* [[AMOS Getting Started]]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=134326 Download]<br />
* [http://sourceforge.net/projects/amos SourceForge project page]<br />
<br />
<br />
== Announcements ==<br />
<br />
* August 5, 2011 - [http://sourceforge.net/projects/amos/files/amos/3.1.0/ Version 3.1.0] of AMOS released!<br />
* August 2, 2011 - [http://sourceforge.net/projects/amos/files/sample_data/ AMOS Sample Data] posted<br />
* December 7, 2010 - [http://sourceforge.net/projects/amos/files/amos/3.0.0/ Version 3.0.0] of AMOS released!<br />
<br />
<br />
== Documentation ==<br />
<br />
=== Assemblers ===<br />
* [[AMOScmp]] - comparative assembler<br />
* [[AMOScmp-shortReads]] - comparative assembler for short reads (Solexa,454)<br />
* [[AMOScmp-shortReads-alignmentTrimmed]] - comparative assembler for short reads that uses alignment based trimming<br />
* [[minimus]] - basic genome assembler for small datasets<br />
* [[Minimo]] - the minimus assembler with many more options: short read support, variable stringency, strand-specificity, various outputs formats<br />
* [[minimus2]] - basic genome assembler for two datasets; can also be used as an assembly merge pipeline<br />
* [[minimus2-blat]] - Same as minimus2 but uses BLAT instead of Nucmer for added speed<br />
<br />
=== Validation and Visualization ===<br />
* [[Hawkeye]] - assembly viewer<br />
* [[amosvalidate]] - assembly forensics<br />
* [[FRCurve]] - Feature-Response Curve<br />
* [[Benchmark]] - assembly benchmark data<br />
<br />
=== Scaffolding ===<br />
* [[Bambus]] - Open source standalone hierarchical scaffolding<br />
* [[Bambus2]] - Scaffolding Polymorphic Genomes and Metagenomes<br />
<br />
=== Trimming, Overlapping, & Error Correction ===<br />
* [[Figaro]] - statistical vector trimmer<br />
* [[UMD Overlapper]] - High quality overlap computations<br />
* [[KI Overlapper]] - Repeat aware overlapper<br />
* [[AutoEditor]] - Automatic correction of genome sequencing errors<br />
* [[FastqQC]] - Read composition and quality<br />
<br />
=== Utilities ===<br />
* [[File conversion utilities]] - converting data to and from AMOS<br />
* [[AMOS Utilities | AMOS Utilities]] - general utilities<br />
* [[runAmos]] - Pipeline executor<br />
<br />
=== AMOS Development ===<br />
* [[Programmer's guide]] - Getting started with the Source code<br />
* [[Infrastructure]] - Developer level details<br />
* [[Wiki guide]] - Guide for editing the wiki<br />
<br />
=== Assembly Tutorials ===<br />
* [http://www.cbcb.umd.edu/research/assembly_primer.shtml Assembly primer] - overview of genome assembly.<br />
* [http://www.cbcb.umd.edu/research/contig_representation.shtml Representing assemblies (not just in AMOS)]<br />
* [http://wgs-assembler.sourceforge.net Running Celera Assembler]<br />
<br />
<br />
Additional documentation in development through the [[AMOS Documentation Project]]<br />
<br />
<br />
== Download == <br />
The AMOS source if freely available for download from the File Release Section of our SourceForge project page. Please refer to the COPYING license included in the package for a description of the Artistic License, the same OSI certified open source license used by Perl and countless other packages. Not all of the above packages are included with the standard AMOS distribution, please see the homepage for the software you wish to download to verify that it is included with the AMOS source distribution.<br />
<br />
[http://sourceforge.net/project/showfiles.php?group_id=134326 Download from SourceForge]<br />
<br />
<br />
== Consortium members ==<br />
<br />
There have been numerous positive responses regarding the AMOS initiative, and we expect the list of involved organizations to grow significantly as the project matures. Please contact us if you want to join. The groups currently involved with the development of AMOS are listed below, along with their responsibilities and areas of expertise.<br />
<br />
* University of Maryland, Center for Bioinformatics and Computational Biology<br />
** project organization and direction<br />
** infrastructure<br />
** consensus<br />
** automated sequence editing<br />
** scaffolding<br />
** overlap detection<br />
** contig construction<br />
<br />
* The Institute for Genomic Research<br />
** production pipelines<br />
** automated finishing tools<br />
** error correction<br />
<br />
* Karolinska Institutet<br />
** overlap detection<br />
** error correction<br />
<br />
* Marine Biological Laboratory - Woods Hole<br />
** graphical interface<br />
** integration of assembly data with analysis (gene, polymorphism, etc.) information<br />
<br />
<br />
== Join the consortium ==<br />
<br />
All interested parties are welcome to join or aid the AMOS consortium. Please address all correspondence via Email to:<br />
<br />
amos-help (at) lists (dot) sourceforge (dot) net<br />
<br />
To receive information regarding new releases and developments, please subscribe to our moderated, low-traffic users' mailing list:<br />
<br />
amos-users (at) lists (dot) sourceforge (dot) net<br />
<br />
<br />
== Bug reports and support ==<br />
<br />
For AMOS bug reports or support requests, please browse our SourceForge project page or Email us at:<br />
<br />
amos-help (at) lists (dot) sourceforge (dot) net<br />
<br />
<br />
<br />
== Acknowledgements ==<br />
<br />
The AMOS consortium would like to thank the following organizations for their funding and/or support:<br />
* The National Institutes of Health - grants R01-LM06845, N01-AI-15447<br />
* The National Science Foundation - grants IIS-9902923, IIS-9820497<br />
* Department of Homeland Security - cooperative agreement W81XWH-05-2-0051<br />
* SourceForge.net</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/AMOS_Getting_StartedAMOS Getting Started2011-07-22T17:58:20Z<p>Ddsommer: /* Downloading the development version */</p>
<hr />
<div>{{TOC}}<br />
<br />
Is AMOS an assembler? is one of the first questions we are asked. The short answer is no. AMOS is not an assembler, rather a software infrastructure for developing assembly tools. If you are only interested in running an off-the-shelf assembler on your shotgun data, do not despair, AMOS provides two such assemblers: AMOScmp - a comparative assembler; and Minimus - a basic assembler for small datasets. However it is important to realize that, with a little bit of programming, you can use AMOS to put together your own shotgun assembler customized for the specific characteristics of your data. <br />
<br />
This page will provide you with the basic information needed to get started using AMOS. Advanced AMOS users can go directly to in-depth resources from the main page [[AMOS]].<br />
<br />
== Downloading AMOS ==<br />
AMOS can be downloaded from Sourceforge using the following link: [http://sourceforge.net/project/showfiles.php?group_id=134326 http://sourceforge.net/project/showfiles.php?group_id=134326]<br />
<br />
No need to remember this URL as you can easily reach it from the [AMOS main page].<br />
<br />
This link will bring you to the Sourceforge download page for our project. While older versions of our code are also available for download from this page we recommend you download the latest version to take advantage of the full functionality of the code.<br />
<br />
AMOS is released as a source-code package, with the exception of the OSX version of the assembly viewer Hawkeye, that can be downloaded as a binary from the File Release section of the download page. Instructions for compiling and installing AMOS are provided below. <br />
<br />
=== Downloading the development version ===<br />
<br />
If you want the bleeding-edge of AMOS, e.g. to edit the source code, you should download the development version of AMOS using CVS following the directions here: [http://sourceforge.net/scm/?type=git&group_id=134326 http://sourceforge.net/scm/?type=git&group_id=134326]<br />
<br />
Or in short:<br />
git clone git://amos.git.sourceforge.net/gitroot/amos/amos<br />
<br />
== Installing AMOS ==<br />
After reading this section make sure you also read the INSTALL file distributed with AMOS. This file may contain information pertaining to the latest version of AMOS that is not included here.<br />
<br />
=== Installing the development version ===<br />
<br />
The first step to install the CVS version of AMOS is to type:<br />
./bootstrap<br />
<br />
Then proceed with the instructions for the normal installation below.<br />
<br />
=== Normal installation ===<br />
The AMOS source package has a name like: amos-1.4.5.tar.gz where 1.4.5 is the version of the code. Once you untar this file (using "tar -xzf amos-1.4.5.tar.gz" in Linux, or "gunzip -d amos-1.4.5.tar.gz | tar xf -" in other flavors of Unix) you will find the current AMOS distribution in a directory named amos-1.4.5. The next steps assume you have cd'd into this directory.<br />
<br />
AMOS uses the [http://www.gnu.org/software/autoconf GNU autoconf] package to reduce cross-platform compatibility issues. Before compiling the code you will need to run the configure script that will probe your system for the locations of all software packages required by AMOS.<br />
<br />
By simply running:<br />
<br />
./configure<br />
<br />
you will prepare AMOS to be installed in the directory hosting the source package. This is OK if you are just testing AMOS. We recommend, however, that you provide the configure script with a more permanent home for AMOS, e.g.:<br />
<br />
./configure --prefix=/usr/local/AMOS<br />
<br />
will ultimately lead the AMOS directory hierarchy to be installed underneath /usr/local/. <br />
<br />
After running configure, make sure you check the messages left on your screen to make sure no errors occured. Errors during the configure step can lead to an incomplete build.<br />
<br />
To compile the code you need to simply run:<br />
<br />
make<br />
<br />
followed by<br />
<br />
make install<br />
<br />
to install AMOS into the directory selected with the --prefix option to configure. <br />
<br />
Normally, these steps are sufficient to install AMOS on most UNIX systems. If you encounter errors during configuration or compilation, or if you are trying to install AMOS on an OSX or Cygwin system, please read the following sub-sections.<br />
<br />
<br />
=== Specifying the location of dependencies ===<br />
If the configure script gives you a message like:<br />
<br />
WARNING! nucmer was not found but is required to run AMOScmp<br />
install nucmer if planning on using AMOScmp<br />
<br />
you either have not installed the [http://mummer.sourceforge.net/ MUMmer] package, or you have installed it in a location where the configure script cannot find it. MUMmer (the nucmer program in particular) is required by the comparative assembler [[AMOScmp]].<br />
<br />
To remedy this situation, please install MUMmer following instructions found at [http://mummer.sourceforge.net http://mummer.sourceforge.net]. <br />
<br />
If MUMmer is already installed, but configure cannot find it, you can specify the location of the nucmer program by setting the environment variably NUCMER, e.g.:<br />
<br />
NUCMER=/usr/local/bin/mummer/nucmer<br />
export NUCMER<br />
<br />
in a "traditional" shell (sh, bash, ksh, etc.), or<br />
<br />
setenv NUCMER /usr/local/bin/mummer/nucmer<br />
<br />
in csh or tcsh. Of course you'll need to replace /usr/local/bin/mummer/nucmer with the actual location of this program on your system.<br />
Specifying the location of the QT library<br />
On most Unix installations (see below for OSX and Cygwin), the QT library should be properly installed and AMOS will make without any problems. If, however, you notice a message like:<br />
<br />
WARNING! Qt3 toolkit was not found but is required to run AMOS GUIs<br />
<br />
the configure process was not able to find the QT library on your system. Check with your system administrator to have this toolkit installed on your system. If, however, you are certain the toolkit is installed, but AMOS still didn't find it, you can directly specify the location of the toolkit directory, or specifically the include, bin, and lib directories, where QT is installed, and the name of the library file, using the following options to the configure script:<br />
<br />
--with-Qt-dir<br />
--with-Qt-include_dir<br />
--with-Qt-lib_dir<br />
--with-Qt-bin_dir<br />
--with-Qt-lib<br />
<br />
Similarly, if you get the message:<br />
<br />
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)<br />
<br />
try specifying the location of Boost with the option:<br />
<br />
--with-Boost-dir<br />
<br />
=== Debian and Ubuntu installation ===<br />
[[Debian installation]]<br />
<br />
=== Fedora, RedHat, CentOS installation ===<br />
[[Fedora installation]]<br />
<br />
=== Mac OS X installation ===<br />
<br />
[[OSX installation]]<br />
<br />
=== Cygwin installation ===<br />
[[Cygwin installation]]<br />
<br />
== Running AMOS ==<br />
<br />
=== Basic AMOS concepts ===<br />
AMOS consists of a collection of modules that operate on a central data-structure called a bank. A bank is really just a directory that contains a database (organized as a collection of indexed files) comprising assembly related objects such as reads, contigs, scaffolds, etc. The modules thus communicate with each other by making changes to the bank. For example, an assembler might consist of three modules: an overlapper, a contigger, and a multi-aligner. The overlapper will first read the shotgun reads from the bank, compare them to each other and write back to the bank a list of overlaps, i.e. pairs of reads that match each other. The contigger then reads the collection of overlaps and makes sense out of it, by producing a layout of the reads that is consistent with most of the observed overlaps. The contigger then writes these contigs (contiguous chunks of the genome) to the bank. Finally, the multi-aligner reads from the bank both the reads and the contigs, builds a multiple alignment of the reads, using as a guide the layout of the reads produced by the contigger, then updates the contigs with the detailed alignment information. Thus, the three programs were able to communicate with each other using the bank as an intermediate storage space. If this litle description didn't make much sense to you, check out our [http://www.cbcb.umd.edu/research/assembly_primer.shtml Genome Assembly Primer]. It also has pointers to future reading.<br />
<br />
Objects in the bank may be identified by one, or both of the following identifiers: IID (internal identifier) - an integer identifier, internal to AMOS; and EID (external identifier) - a string representing some external identifier of the record, e.g. the original name of a sequencing read. Both identifiers must be unique for a specific object type, but may be shared by multiple objects. For example, there can only be one contig with an IID equal to 1, however there can be both a contig, and a read, and an overlap, all with the IID = 1.<br />
Message files<br />
The AMOS banks are not the only mechanism for AMOS modules to communicate with each other, and to the "outside world". AMOS also uses a flat-file format (AMOS message files) inspired by the format used in Celera Assembler. This format is generally used as an intermediate format for converting to and from external file formats. The AMOS message files are then used to populate the data-structures present in a bank. <br />
<br />
For more details on the AMOS message file format check out the [[Infrastructure]] pages. The use of message files will be described in more detail in the remainder of this tutorial.<br />
<br />
<br />
==== Reading and writing banks ====<br />
To learn how to generate AMOS message files check out the section called Creating inputs for AMOS. Assuming you already have an AMOS message file, most of the modules will require that the information from this file be loaded into a bank. This section describes the commands used to transfer information between a bank and the message file.<br />
<br />
The command bank-transact can be used to load a message file into a bank. In its simplest invocation:<br />
<br />
bank-transact -b mybank -m mymessagefile<br />
<br />
bank-transact loads the messages in mymessagefile into the bank mybank. Note that this invocation assume the bank already exists, and bank-transact will fail otherwise. When creating a new bank you can run:<br />
<br />
bank-transact -c -b mybank -m mymessagefile<br />
<br />
The option -c stands for "create". By also providing the option -f (force), the bank will be overwritten if it already exists.<br />
<br />
The contents of a bank can be output into a flat-file format with the command:<br />
<br />
bank-report -b mybank<br />
<br />
By default bank-report outputs all the data in the bank. The output can be restricted to certain message types by providing the 3 letter codes of the messages to be output, e.g:<br />
<br />
bank-report -b mybank CTG RED<br />
<br />
will output all the contigs (CTG) and read (RED) records. In addition bank-report allows the user to specify a list of EIDs (option -E) or a list of IIDs (option -I) that will be reported.<br />
<br />
<br />
==== Bank locking ====<br />
To allow concurrent access to the bank, AMOS programs lock the bank while the operate on it. There are two types of locks: for reading, and writing. If a bank is locked for reading, other read accesses are allowed but no writes. If a bank is locked for writing, no concurrent accesses are allowed. Some of the AMOS tools (such as the viewer Hawkeye), have an option to load a bank in "inspect" mode, i.e. the code ignores any locks placed on the bank.<br />
<br />
In certain situations, if a program accessing the bank crashes, the bank may remain locked, prohibiting further access. All existing locks can be removed with the command (make sure that another user is not accessing the same bank):<br />
<br />
bank-unlock mybank<br />
<br />
<br />
==== Bank versions ====<br />
The specific format of the AMOS bank is closely related to the current version of the AMOS software. The banks are not backward compatible, i.e., a bank produced by AMOS 1.0 will not be readable by AMOS 1.5. A simple solution for reading a bank created by an older version of AMOS is to output the contents of the bank using bank-report (the AMOS distribution contains old versions of the bank-report code, e.g. bank-report-1.1) , then reload the bank with the most recent bank-transact command.<br />
<br />
<br />
==== Pipelines ====<br />
As it has hopefully become clear from the introduction to AMOS above, most genome assembly tasks involve the sequential execution of several modules, in an assembly line (or pipeline) fashion. AMOS provides a mechanism for quickly putting together simple pipelines. By "simple" we mean situations where the specific assembly task involves running several programs in order, without the need for more complex control structures such as "if" statements or loops. To implement complex pipelines you will have to rely on Perl or another complex programming language. <br />
<br />
An AMOS pipelines are described in a simple interpreted language, and consist of a series of steps that are executed in order. The steps are meant to provide a logical breakdown of the individual assembly tasks, representing the execution of one or more programs. Each step in a pipeline is identified by a step number (a throw-back to the days of the Basic language) providing the user with a mechanism to execute only some of the steps of a pipeline. <br />
<br />
To learn more about AMOS pipelines and how to write them, check out the documentation for [[runAmos]] (the pipeline executor), or check out one of the pipelines distributed with AMOS (AMOScmp and minimus are good starting points).<br />
<br />
=== Creating inputs for AMOS ===<br />
The inputs to most AMOS programs must be provided in the AMOS message format. For help converting non-AMOS file formats into message files see the [[File conversion utilities]].<br />
<br />
<br />
=== Running AMOScmp ===<br />
AMOScmp is a comparative assembler that can be used to assemble reads from one genome (called the target) using as a template the sequence of a related genome (called the reference). Read the AMOScmp documentation for a detailed description of this program.<br />
<br />
By default, running AMOScmp as follows:<br />
<br />
AMOScmp prefix<br />
<br />
assumes that the target is provided in the AMOS message file prefix.afg, and the reference in the file prefix.1con. To use different file locations, you can set the variables TGT and REF, either directly within the AMOScmp script, or on the command line:<br />
<br />
AMOScmp -D "TGT=mytarget.afg" -D "REF=myreference.1con" prefix<br />
<br />
The prefix must still be provided as it is used to generate the name of the output files.<br />
<br />
AMOScmp will populate a bank named prefix.bnk, and will load into it a set of contigs, as well as a scaffold, linking together contigs that are adjacent along the reference. In addition, AMOScmp outputs the set of contigs as both a multi-FASTA file prefix.fasta, and a TIGR .contig file prefix.contig. Note that the consensus of the contigs (reported in the FASTA file) is generated from the target genome, and may differ from the reference genome (after all, the goal of the assembler is to assemble the target). In fact, AMOScmp uses sophisticated algorithms for detecting differences between the target and reference in order to prevent misassemblies. For more information refer to:<br />
<br />
M. Pop, A. Phillippy, A.L. Delcher and S.L. Salzberg. [http://www.cbcb.umd.edu/papers/Pop%20et%20al%20Comparative.pdf Comparative genome assembly]. Briefings in Bioinformatics. 5(3), pp. 237-248, 2004.<br />
<br />
<br />
=== Running minimus ===<br />
Minimus is a basic genome assembler that can be used for small assembly jobs (e.g. a single gene, or a viral genome). Minimus is currently used as a central component of the Influenza A sequencing pipeline at The Institute for Genomic Research. Read the [[minimus]] documentation for more information.<br />
<br />
To run minimus you must provide a set of shotgun reads in an AMOS message file. Running:<br />
<br />
minimus prefix<br />
<br />
assumes the input is in file prefix.afg. After running, minimus populates the bank prefix.bnk with a set of contigs, furthermore it reports the contigs in both a FASTA file (prefix.fasta) and a TIGR .contig file (prefix.contig). Note that minimus does not use mate-pairs. In essence it is, in Celera Assembler terminology, a unitigger. Any mate-pair information provided in the .afg will be silently ignored.<br />
<br />
<br />
=== Viewing the result of an assembly ===<br />
The content of a bank can be viewed with a program called Hawkeye:<br />
<br />
hawkeye mybank<br />
<br />
For detailed information on how to use Hawkeye, refer to the [[Hawkeye]] documentation.<br />
<br />
<br />
=== Validating assemblies ===<br />
Even the best genome assemblers sometimes make mistakes. AMOS provides a mechanism to run several checks on the output of an assembler (assuming the data are already stored in a bank), through a script called amosvalidate. Amosvalidate runs through the assembly and identifies several types of inconsistencies, such as clusters of SNPs in the assembled reads, clusters of mate-pairs that are too close or too far from each other (with respect to the estimated library sizes), and unassembled reads that do not properly match the assembly. A full description of these measures is beyond the scope of this document. We are currently submitting a manuscript describing the tools included in amosvalidate and will update this page when it gets published.<br />
<br />
All the potential assembly problems identified by amosvalidate are written back into the bank as features, i.e ranges along the assembly. Each feature is tagged with the problem that was identified in that region. Typically, users then load the assembly in the Hawkeye viewer and examine the assembly in the tagged regions. Alternatively, the features may be extracted from the bank and processed automatically by specialized software (e.g. several assemblies of a same genome can be compared by the number of features identified in the assembly - the assembly with fewer features is likely "better"). <br />
<br />
Running amosvalidate is as simple as:<br />
<br />
amosvalidate prefix<br />
<br />
where prefix.bnk is the location of the bank.<br />
<br />
== Getting help ==<br />
To report bugs in AMOS, or to get help, email us at:<br />
<br />
amos-help (at) lists (dot) sourceforget (dot) net<br />
<br />
To receive information regarding new releases and developments, please [http://lists.sourceforge.net/lists/listinfo/amos-users subscribe] to our moderated, low-traffic users' mailing list:<br />
<br />
amos-users (at) lists (dot) sourceforget (dot) net</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/AMOS_Getting_StartedAMOS Getting Started2011-07-22T17:56:28Z<p>Ddsommer: /* Downloading the development version */</p>
<hr />
<div>{{TOC}}<br />
<br />
Is AMOS an assembler? is one of the first questions we are asked. The short answer is no. AMOS is not an assembler, rather a software infrastructure for developing assembly tools. If you are only interested in running an off-the-shelf assembler on your shotgun data, do not despair, AMOS provides two such assemblers: AMOScmp - a comparative assembler; and Minimus - a basic assembler for small datasets. However it is important to realize that, with a little bit of programming, you can use AMOS to put together your own shotgun assembler customized for the specific characteristics of your data. <br />
<br />
This page will provide you with the basic information needed to get started using AMOS. Advanced AMOS users can go directly to in-depth resources from the main page [[AMOS]].<br />
<br />
== Downloading AMOS ==<br />
AMOS can be downloaded from Sourceforge using the following link: [http://sourceforge.net/project/showfiles.php?group_id=134326 http://sourceforge.net/project/showfiles.php?group_id=134326]<br />
<br />
No need to remember this URL as you can easily reach it from the [AMOS main page].<br />
<br />
This link will bring you to the Sourceforge download page for our project. While older versions of our code are also available for download from this page we recommend you download the latest version to take advantage of the full functionality of the code.<br />
<br />
AMOS is released as a source-code package, with the exception of the OSX version of the assembly viewer Hawkeye, that can be downloaded as a binary from the File Release section of the download page. Instructions for compiling and installing AMOS are provided below. <br />
<br />
=== Downloading the development version ===<br />
<br />
If you want the bleeding-edge of AMOS, e.g. to edit the source code, you should download the development version of AMOS using CVS following the directions here: [http://sourceforge.net/scm/?type=cvs&group_id=134326 http://sourceforge.net/scm/?type=cvs&group_id=134326]<br />
<br />
Or in short:<br />
git clone git://amos.git.sourceforge.net/gitroot/amos/amos<br />
<br />
== Installing AMOS ==<br />
After reading this section make sure you also read the INSTALL file distributed with AMOS. This file may contain information pertaining to the latest version of AMOS that is not included here.<br />
<br />
=== Installing the development version ===<br />
<br />
The first step to install the CVS version of AMOS is to type:<br />
./bootstrap<br />
<br />
Then proceed with the instructions for the normal installation below.<br />
<br />
=== Normal installation ===<br />
The AMOS source package has a name like: amos-1.4.5.tar.gz where 1.4.5 is the version of the code. Once you untar this file (using "tar -xzf amos-1.4.5.tar.gz" in Linux, or "gunzip -d amos-1.4.5.tar.gz | tar xf -" in other flavors of Unix) you will find the current AMOS distribution in a directory named amos-1.4.5. The next steps assume you have cd'd into this directory.<br />
<br />
AMOS uses the [http://www.gnu.org/software/autoconf GNU autoconf] package to reduce cross-platform compatibility issues. Before compiling the code you will need to run the configure script that will probe your system for the locations of all software packages required by AMOS.<br />
<br />
By simply running:<br />
<br />
./configure<br />
<br />
you will prepare AMOS to be installed in the directory hosting the source package. This is OK if you are just testing AMOS. We recommend, however, that you provide the configure script with a more permanent home for AMOS, e.g.:<br />
<br />
./configure --prefix=/usr/local/AMOS<br />
<br />
will ultimately lead the AMOS directory hierarchy to be installed underneath /usr/local/. <br />
<br />
After running configure, make sure you check the messages left on your screen to make sure no errors occured. Errors during the configure step can lead to an incomplete build.<br />
<br />
To compile the code you need to simply run:<br />
<br />
make<br />
<br />
followed by<br />
<br />
make install<br />
<br />
to install AMOS into the directory selected with the --prefix option to configure. <br />
<br />
Normally, these steps are sufficient to install AMOS on most UNIX systems. If you encounter errors during configuration or compilation, or if you are trying to install AMOS on an OSX or Cygwin system, please read the following sub-sections.<br />
<br />
<br />
=== Specifying the location of dependencies ===<br />
If the configure script gives you a message like:<br />
<br />
WARNING! nucmer was not found but is required to run AMOScmp<br />
install nucmer if planning on using AMOScmp<br />
<br />
you either have not installed the [http://mummer.sourceforge.net/ MUMmer] package, or you have installed it in a location where the configure script cannot find it. MUMmer (the nucmer program in particular) is required by the comparative assembler [[AMOScmp]].<br />
<br />
To remedy this situation, please install MUMmer following instructions found at [http://mummer.sourceforge.net http://mummer.sourceforge.net]. <br />
<br />
If MUMmer is already installed, but configure cannot find it, you can specify the location of the nucmer program by setting the environment variably NUCMER, e.g.:<br />
<br />
NUCMER=/usr/local/bin/mummer/nucmer<br />
export NUCMER<br />
<br />
in a "traditional" shell (sh, bash, ksh, etc.), or<br />
<br />
setenv NUCMER /usr/local/bin/mummer/nucmer<br />
<br />
in csh or tcsh. Of course you'll need to replace /usr/local/bin/mummer/nucmer with the actual location of this program on your system.<br />
Specifying the location of the QT library<br />
On most Unix installations (see below for OSX and Cygwin), the QT library should be properly installed and AMOS will make without any problems. If, however, you notice a message like:<br />
<br />
WARNING! Qt3 toolkit was not found but is required to run AMOS GUIs<br />
<br />
the configure process was not able to find the QT library on your system. Check with your system administrator to have this toolkit installed on your system. If, however, you are certain the toolkit is installed, but AMOS still didn't find it, you can directly specify the location of the toolkit directory, or specifically the include, bin, and lib directories, where QT is installed, and the name of the library file, using the following options to the configure script:<br />
<br />
--with-Qt-dir<br />
--with-Qt-include_dir<br />
--with-Qt-lib_dir<br />
--with-Qt-bin_dir<br />
--with-Qt-lib<br />
<br />
Similarly, if you get the message:<br />
<br />
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)<br />
<br />
try specifying the location of Boost with the option:<br />
<br />
--with-Boost-dir<br />
<br />
=== Debian and Ubuntu installation ===<br />
[[Debian installation]]<br />
<br />
=== Fedora, RedHat, CentOS installation ===<br />
[[Fedora installation]]<br />
<br />
=== Mac OS X installation ===<br />
<br />
[[OSX installation]]<br />
<br />
=== Cygwin installation ===<br />
[[Cygwin installation]]<br />
<br />
== Running AMOS ==<br />
<br />
=== Basic AMOS concepts ===<br />
AMOS consists of a collection of modules that operate on a central data-structure called a bank. A bank is really just a directory that contains a database (organized as a collection of indexed files) comprising assembly related objects such as reads, contigs, scaffolds, etc. The modules thus communicate with each other by making changes to the bank. For example, an assembler might consist of three modules: an overlapper, a contigger, and a multi-aligner. The overlapper will first read the shotgun reads from the bank, compare them to each other and write back to the bank a list of overlaps, i.e. pairs of reads that match each other. The contigger then reads the collection of overlaps and makes sense out of it, by producing a layout of the reads that is consistent with most of the observed overlaps. The contigger then writes these contigs (contiguous chunks of the genome) to the bank. Finally, the multi-aligner reads from the bank both the reads and the contigs, builds a multiple alignment of the reads, using as a guide the layout of the reads produced by the contigger, then updates the contigs with the detailed alignment information. Thus, the three programs were able to communicate with each other using the bank as an intermediate storage space. If this litle description didn't make much sense to you, check out our [http://www.cbcb.umd.edu/research/assembly_primer.shtml Genome Assembly Primer]. It also has pointers to future reading.<br />
<br />
Objects in the bank may be identified by one, or both of the following identifiers: IID (internal identifier) - an integer identifier, internal to AMOS; and EID (external identifier) - a string representing some external identifier of the record, e.g. the original name of a sequencing read. Both identifiers must be unique for a specific object type, but may be shared by multiple objects. For example, there can only be one contig with an IID equal to 1, however there can be both a contig, and a read, and an overlap, all with the IID = 1.<br />
Message files<br />
The AMOS banks are not the only mechanism for AMOS modules to communicate with each other, and to the "outside world". AMOS also uses a flat-file format (AMOS message files) inspired by the format used in Celera Assembler. This format is generally used as an intermediate format for converting to and from external file formats. The AMOS message files are then used to populate the data-structures present in a bank. <br />
<br />
For more details on the AMOS message file format check out the [[Infrastructure]] pages. The use of message files will be described in more detail in the remainder of this tutorial.<br />
<br />
<br />
==== Reading and writing banks ====<br />
To learn how to generate AMOS message files check out the section called Creating inputs for AMOS. Assuming you already have an AMOS message file, most of the modules will require that the information from this file be loaded into a bank. This section describes the commands used to transfer information between a bank and the message file.<br />
<br />
The command bank-transact can be used to load a message file into a bank. In its simplest invocation:<br />
<br />
bank-transact -b mybank -m mymessagefile<br />
<br />
bank-transact loads the messages in mymessagefile into the bank mybank. Note that this invocation assume the bank already exists, and bank-transact will fail otherwise. When creating a new bank you can run:<br />
<br />
bank-transact -c -b mybank -m mymessagefile<br />
<br />
The option -c stands for "create". By also providing the option -f (force), the bank will be overwritten if it already exists.<br />
<br />
The contents of a bank can be output into a flat-file format with the command:<br />
<br />
bank-report -b mybank<br />
<br />
By default bank-report outputs all the data in the bank. The output can be restricted to certain message types by providing the 3 letter codes of the messages to be output, e.g:<br />
<br />
bank-report -b mybank CTG RED<br />
<br />
will output all the contigs (CTG) and read (RED) records. In addition bank-report allows the user to specify a list of EIDs (option -E) or a list of IIDs (option -I) that will be reported.<br />
<br />
<br />
==== Bank locking ====<br />
To allow concurrent access to the bank, AMOS programs lock the bank while the operate on it. There are two types of locks: for reading, and writing. If a bank is locked for reading, other read accesses are allowed but no writes. If a bank is locked for writing, no concurrent accesses are allowed. Some of the AMOS tools (such as the viewer Hawkeye), have an option to load a bank in "inspect" mode, i.e. the code ignores any locks placed on the bank.<br />
<br />
In certain situations, if a program accessing the bank crashes, the bank may remain locked, prohibiting further access. All existing locks can be removed with the command (make sure that another user is not accessing the same bank):<br />
<br />
bank-unlock mybank<br />
<br />
<br />
==== Bank versions ====<br />
The specific format of the AMOS bank is closely related to the current version of the AMOS software. The banks are not backward compatible, i.e., a bank produced by AMOS 1.0 will not be readable by AMOS 1.5. A simple solution for reading a bank created by an older version of AMOS is to output the contents of the bank using bank-report (the AMOS distribution contains old versions of the bank-report code, e.g. bank-report-1.1) , then reload the bank with the most recent bank-transact command.<br />
<br />
<br />
==== Pipelines ====<br />
As it has hopefully become clear from the introduction to AMOS above, most genome assembly tasks involve the sequential execution of several modules, in an assembly line (or pipeline) fashion. AMOS provides a mechanism for quickly putting together simple pipelines. By "simple" we mean situations where the specific assembly task involves running several programs in order, without the need for more complex control structures such as "if" statements or loops. To implement complex pipelines you will have to rely on Perl or another complex programming language. <br />
<br />
An AMOS pipelines are described in a simple interpreted language, and consist of a series of steps that are executed in order. The steps are meant to provide a logical breakdown of the individual assembly tasks, representing the execution of one or more programs. Each step in a pipeline is identified by a step number (a throw-back to the days of the Basic language) providing the user with a mechanism to execute only some of the steps of a pipeline. <br />
<br />
To learn more about AMOS pipelines and how to write them, check out the documentation for [[runAmos]] (the pipeline executor), or check out one of the pipelines distributed with AMOS (AMOScmp and minimus are good starting points).<br />
<br />
=== Creating inputs for AMOS ===<br />
The inputs to most AMOS programs must be provided in the AMOS message format. For help converting non-AMOS file formats into message files see the [[File conversion utilities]].<br />
<br />
<br />
=== Running AMOScmp ===<br />
AMOScmp is a comparative assembler that can be used to assemble reads from one genome (called the target) using as a template the sequence of a related genome (called the reference). Read the AMOScmp documentation for a detailed description of this program.<br />
<br />
By default, running AMOScmp as follows:<br />
<br />
AMOScmp prefix<br />
<br />
assumes that the target is provided in the AMOS message file prefix.afg, and the reference in the file prefix.1con. To use different file locations, you can set the variables TGT and REF, either directly within the AMOScmp script, or on the command line:<br />
<br />
AMOScmp -D "TGT=mytarget.afg" -D "REF=myreference.1con" prefix<br />
<br />
The prefix must still be provided as it is used to generate the name of the output files.<br />
<br />
AMOScmp will populate a bank named prefix.bnk, and will load into it a set of contigs, as well as a scaffold, linking together contigs that are adjacent along the reference. In addition, AMOScmp outputs the set of contigs as both a multi-FASTA file prefix.fasta, and a TIGR .contig file prefix.contig. Note that the consensus of the contigs (reported in the FASTA file) is generated from the target genome, and may differ from the reference genome (after all, the goal of the assembler is to assemble the target). In fact, AMOScmp uses sophisticated algorithms for detecting differences between the target and reference in order to prevent misassemblies. For more information refer to:<br />
<br />
M. Pop, A. Phillippy, A.L. Delcher and S.L. Salzberg. [http://www.cbcb.umd.edu/papers/Pop%20et%20al%20Comparative.pdf Comparative genome assembly]. Briefings in Bioinformatics. 5(3), pp. 237-248, 2004.<br />
<br />
<br />
=== Running minimus ===<br />
Minimus is a basic genome assembler that can be used for small assembly jobs (e.g. a single gene, or a viral genome). Minimus is currently used as a central component of the Influenza A sequencing pipeline at The Institute for Genomic Research. Read the [[minimus]] documentation for more information.<br />
<br />
To run minimus you must provide a set of shotgun reads in an AMOS message file. Running:<br />
<br />
minimus prefix<br />
<br />
assumes the input is in file prefix.afg. After running, minimus populates the bank prefix.bnk with a set of contigs, furthermore it reports the contigs in both a FASTA file (prefix.fasta) and a TIGR .contig file (prefix.contig). Note that minimus does not use mate-pairs. In essence it is, in Celera Assembler terminology, a unitigger. Any mate-pair information provided in the .afg will be silently ignored.<br />
<br />
<br />
=== Viewing the result of an assembly ===<br />
The content of a bank can be viewed with a program called Hawkeye:<br />
<br />
hawkeye mybank<br />
<br />
For detailed information on how to use Hawkeye, refer to the [[Hawkeye]] documentation.<br />
<br />
<br />
=== Validating assemblies ===<br />
Even the best genome assemblers sometimes make mistakes. AMOS provides a mechanism to run several checks on the output of an assembler (assuming the data are already stored in a bank), through a script called amosvalidate. Amosvalidate runs through the assembly and identifies several types of inconsistencies, such as clusters of SNPs in the assembled reads, clusters of mate-pairs that are too close or too far from each other (with respect to the estimated library sizes), and unassembled reads that do not properly match the assembly. A full description of these measures is beyond the scope of this document. We are currently submitting a manuscript describing the tools included in amosvalidate and will update this page when it gets published.<br />
<br />
All the potential assembly problems identified by amosvalidate are written back into the bank as features, i.e ranges along the assembly. Each feature is tagged with the problem that was identified in that region. Typically, users then load the assembly in the Hawkeye viewer and examine the assembly in the tagged regions. Alternatively, the features may be extracted from the bank and processed automatically by specialized software (e.g. several assemblies of a same genome can be compared by the number of features identified in the assembly - the assembly with fewer features is likely "better"). <br />
<br />
Running amosvalidate is as simple as:<br />
<br />
amosvalidate prefix<br />
<br />
where prefix.bnk is the location of the bank.<br />
<br />
== Getting help ==<br />
To report bugs in AMOS, or to get help, email us at:<br />
<br />
amos-help (at) lists (dot) sourceforget (dot) net<br />
<br />
To receive information regarding new releases and developments, please [http://lists.sourceforge.net/lists/listinfo/amos-users subscribe] to our moderated, low-traffic users' mailing list:<br />
<br />
amos-users (at) lists (dot) sourceforget (dot) net</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:42:50Z<p>Ddsommer: /* Overview */</p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
== Download ==<br />
NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
* Two ways to find the reference proteins:<br />
** Do a draft annotation of the genome using a annotation pipline. ABBA will not annotate your assembly.<br />
** Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:39:34Z<p>Ddsommer: /* Download */</p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
* Two ways to find the reference proteins:<br />
** Do a draft annotation of the genome using a annotation pipline. ABBA will not annotate your assembly.<br />
** Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:38:38Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
* Two ways to find the reference proteins:<br />
** Do a draft annotation of the genome<br />
** Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:37:47Z<p>Ddsommer: /* Download */</p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
IMPORTANT TO NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
Two ways to find the reference proteins:<br />
** Do a draft annotation of the genome<br />
** Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:37:03Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
IMPORTANT TO NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
Two ways to find the reference proteins:<br />
1. Do a draft annotation of the genome<br />
2. Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:35:10Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
Two ways to find the reference proteins:<br />
1. Do a draft annotation of the genome<br />
2. Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
IMPORTANT TO NOTE : ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T20:34:26Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.<br />
<br />
Two ways to find the reference proteins:<br />
1. Do a draft annotation of the genome<br />
2. Align the draft assembly contigs to a close relative and find where the contig ends intersect protein coding regions.<br />
<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Download ==<br />
<br />
<br />
ABBA is built on top of the AMOS framework but has it's own distribution. The AMOS framework is included in the ABBA tarball and will install with AMOS if you don't already have AMOS installed. The tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
IT IS IMPORTANT TO NOTE: ABBA does protein assembly but doesn't find the reference proteins to assemble. You will need to find the proteins running off the ends of contigs separately and then pass the proteins to ABBA to fill in the gaps.<br />
<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T19:55:28Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. See the journal paper.<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Documentation ==<br />
<br />
Documentation on running ABBA is included in the tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer/abba.tgz<br />
<br />
<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T19:21:19Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. See the journal paper.<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Documentation ==<br />
<br />
Documentation on running ABBA is included in the tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer<br />
<br />
<br />
"NOTE: ABBA relies on other tools in the AMOS package, so you need<br />
to download and install AMOS as well."<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommerhttp://amos.sourceforge.net/wiki/index.php/ABBAABBA2011-02-17T19:13:39Z<p>Ddsommer: </p>
<hr />
<div>ABBA: Assembly Boosted By Amino acid sequences<br />
<br />
== Overview ==<br />
<br />
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. See the journal paper.<br />
<br />
For additional information on short read assembly check the following University of Maryland CBCB web sites:<br />
<br />
* [http://www.cbcb.umd.edu/research/SR-assembly.shtml Genome Assembly with Short Reads]<br />
* [http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml Genome Assembly with Short Reads Tutorial]<br />
<br />
<br />
== Documentation ==<br />
<br />
Documentation on running ABBA is included in the tarball<br />
<br />
<br />
"NOTE: ABBA relies on other tools in the AMOS package, so you need<br />
to download and install AMOS as well."<br />
<br />
== References ==<br />
<br />
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads].<br />
<br />
Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186<br />
<br />
<br />
== Acknowledgements ==<br />
The development of ABBA was supported by the National Institutes of Health under grants [http://www.google.com/search?q=R01-LM06845 R01-LM06845] and [http://www.google.com/search?q=R01-LM007938 R01-LM007938] to SLS.</div>Ddsommer