AMOS WIKI - User contributions [en]

Bambus2

2014-04-07T19:16:25Z

Decaos: updating GFD -> GDE, add link to metAMOS

[http://www.cs.umd.edu/~sergek/ Sergey Koren] and
[http://www.cbcb.umd.edu/~mpop/ Mihai Pop]

Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. The original Bambus package was the first general purpose scaffolders made available as an open source package. We are happy to announce the arrival of Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Getting data into Bambus 2 requires you convert your assembly to AMOS format. Here is my recipe:

[[toAmos]] \
-s my.fa \
-c my.contig \
-m my.mates \
-o my.afg

You need the .fa to list the contigs within the [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Bank2contig#TIGR_Assembler_.2F_GDE_Contig_Format GDE]-like contig file (annoying but true). You don't need accurate sequences in the .fa, you just need something to make the format valid. The .contig and .mates are as expected for [[Bambus]].

The resulting .afg is then 'banked' with:

[[bank-transact]] -c \
-b my.bnk \
-m my.afg

Bambus2 is composed of a series of scripts. For instruction about how to use them see: [[Bambus 2.0/quick start guide]].

'''The easiest way to use/run Bambus2 is to use [http://metamos.readthedocs.org/en/latest/ metAMOS], available on [https://github.com/marbl/metAMOS github].
'''

Alternatively, there is a Python script to facilitate running Bambus2 in one quick command:

goBambus2

which returns:

run: goBambus2 <input reads or contigs or amos bank name> <output prefix> [options]
eg.: goBambus2 example.contigs myoutput --all --contigs
This script is designed to run the Bambus pipeline and takes either reads or contigs plus XML Trace Archive data as input and outputs scaffolds
For further info please contact the Bambus 2 authors: Sergey Koren and Mihai Pop

For example, you could run:

goBambus2 brucella.seq myScaff --all --reads

More information is available at http://www.cbcb.umd.edu/software/bambus/

Bambus 2.0/quick start guide

2014-03-31T13:59:10Z

Decaos: remove broken links

==How to run Bambus 2.0==
'''Caveat:''' Bambus is still being actively developed and the code is currently in the "user beware" and "for experts only" stage.

=== Step 1. Install the AMOS package - Bambus 2.0 is part of it. ===
See [[AMOS Getting Started]].

'''Note:''' since Bambus is still under active development you should pull the latest unofficial release of AMOS directly from the Git repository - see instructions at: [[Programmer's guide]].

=== Step 2. What information you need ===
Bambus needs to know about the contigs produced by the assembler and information about how these contigs are linked to each other. In AMOS terms, the basic information necessary are a list of contigs (http://amos.sourceforge.net/docs/api/classAMOS_1_1Contig__t.html) and a list of contig links (http://amos.sourceforge.net/docs/api/classAMOS_1_1ContigLink__t.html) or contig edges (http://amos.sourceforge.net/docs/api/classAMOS_1_1ContigEdge__t.html - bundles of consistent contig links) indicating the relative placement of pairs of contigs.

These data can either be provided to Bambus directly in the form of a AMOS message file (see [[Message Types]]) or inferred from mate-pair information as described below.

== Running Bambus 2.0 ==
* First, add the .afg file built as described above (for other conversion utilities see: http://sourceforge.net/apps/mediawiki/amos/index.php?title=File_conversion_utilities) to an AMOS bank (flat-file database):
bank-transact -cf myproj.bnk -m myfile.afg

* Use the mate-pair information to construct a collection of contig links.
clk -b myproj.bnk

'''Note:''' that you can also construct these links with your own custom software and upload them into the bank in which case you would skip the "clk" command.

* Bundle the contig links into a collection of contig edges.
Bundler -b myproj.bnk

'''Note:''' as with the clk command you might want to build the contig edges separately and upload them into the bank using your own software.

'''Note:''' the Bundler command also accepts the command line parameter "-t" followed by a list of edge types as defined in src/AMOS/Link_AMOS.hh. Currently the following types are defined: '''M''' - mate-pair, '''O''' - overlap, '''P''' - physical, '''A''' - alignment, '''S''' - synteny, and '''X''' - other.

* Identify genomic repeats and output them to std out
MarkRepeats -b myproj.bnk [-redundancy X -aggressive] > myRepeats

Optional parameters:
:"-redundancy X" only uses contig edges comprising X or more contig links
:"-aggressive" - aggressive repeat identification based on global depth of coverage statistics (default procedure relies on graph analysis rather than coverage statistics)

'''Note:''' this program requires the boost library

* Order and orient contigs according to repeat and link information

'''IMPORTANT:''' several of the operations performed by this program destructively modify the bank (changes cannot be undone). You should make a copy of the bank prior to running OrientContigs.

OrientContigs -b myproj.bnk -prefix myscaff

:"-prefix" specifies the prefix for all output files

Optional parameters:
:"-all" - output unlinked contigs as scaffolds
:"-noreduce" - turns off graph simplification routines (see below)
:"-redundancy X" - same as above - ignore edges with less than X links
:"-repeats filename" - ignores repeats listed in "filename" (one contig ID per line) as generated, e.g. by the MarkRepeats :program described above.
:"-aggressive" - aggressive scaffolding - by default links that are stretched by more than 3 standard deviations are ignored. Aggressive option turns this feature off and tries to reconcile the scaffold as best possible.

* Linearize the scaffolds (if desired). By default Bambus 2 produces non-linear graph-based scaffolds. If fasta output is desired, it is necessary to linearize the scaffolds.
untangle -e myscaff.evidence.xml -s myscaff.out.xml -o myscaff.untangle.xml

* Output fasta result (if desired). This involves two steps, the first to generating the fasta file representing the contigs and the second combines them, separated by Ns, into a scaffold fasta file.
bank2fasta -d -b myproj.bnk > contigs.fasta
printScaff -e myscaff.evidence.xml -s myscaff.untangle.xml -l myscaff.library -f contigs.fasta -merge -o myscaff

== Outputs ==
The output of the OrientContigs program is a collection of scaffolds stored in the bank. The program also generates several files starting with the specified prefix
*myScaff.agp
**The scaffolds generated by the OrientContigs programs in NCBI AGP format
*myScaff.dot
**The scaffolds generated by the OrientContigs program in Graphviz dot format. It can be converted to a PostScript or PDF file using the dot program in the Graphviz package.
*myScaff.evidence.xml
*myScaff.library
*myScaff.out.xml
**The scaffolds generated by the OrientContigs program compatible with the Bambus 1 format.
*myScaff.fasta
**The fasta file of the scaffolds, joined by Ns
*myScaff.stats
**Statistics on the scaffolds generated, including N50 and total span.

=== Scaffold simplifications ===
By default (unless option "-noreduce" is provided) the OrientContigs program simplifies certain
graph patterns:
* simple paths
* bubbles
** These patterns are iteratively merged into single contigs until no additional simplifications can be made.

Bambus2

2011-06-15T15:16:46Z

Decaos: goBambus2.py now available inside current AMOS release, 3.0.1

[http://www.cs.umd.edu/~sergek/ Sergey Koren] and
[http://www.cbcb.umd.edu/~mpop/ Mihai Pop]

Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. The original Bambus package was the first general purpose scaffolders made available as an open source package. We are happy to announce the arrival of Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Getting data into Bambus 2 requires you convert your assembly to AMOS format. Here is my recipe:

[[toAmos]] \
-s my.fa \
-c my.contig \
-m my.mates \
-o my.afg

You need the .fa to list the contigs within the GFD-like contig file (annoying but true). You don't need accurate sequences in the .fa, you just need something to make the format valid. The .contig and .mates are as expected for [[Bambus]].

The resulting .afg is then 'banked' with:

[[bank-transact]] -c \
-b my.bnk \
-m my.afg

Bambus2 is composed of a series of scripts. For instruction about how to use them see: [[Bambus 2.0/quick start guide]].

There is a Python script to facilitate running Bambus2 in one quick command:

goBambus2

which returns:

run: goBambus2 <input reads or contigs or amos bank name> <output prefix> [options]
eg.: goBambus2 example.contigs myoutput --all --contigs
This script is designed to run the Bambus pipeline and takes either reads or contigs plus XML Trace Archive data as input and outputs scaffolds
For further info please contact the Bambus 2 authors: Sergey Koren and Mihai Pop

For example, you could run:

goBambus2 brucella.seq myScaff --all --reads

More information is available at http://www.cbcb.umd.edu/software/bambus/

Minimus

2010-11-09T19:57:57Z

Decaos: /* Basic usage */

== Overview ==

Minimus is one of several assembly pipelines included in the AMOS software package. It is designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.

Minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules which share information through a central file bank:

* [[hash-overlap]] - Computes the overlaps between the reads using a modified version of the Smith-Waterman local alignment algorithm
* [[tigger]] - Uses the read overlaps to generate the layouts of reads representing individual contigs
* [[make-consensus]] - Refines the layouts produced by the tigger to generate accurate multiple alignments within the reads

Minimus uses AMOS message files as both the inputs and the outputs. Please see the [[File conversion utilities]] documentation for more information.

[[minimus2 | Minimus2]] is a modified version of the minimus pipeline designed for merging two sequence sets. Instead of hash-overlap it uses a nucmer based overlap detector which is much faster.

== Documentation ==

Documentation on running minimus is included with the distribution in the /docs subdirectory.

See [[Minimus/README]].

== Examples ==

Examples of a flu assembly and a Zebrafish gene can be found in the test/minimus directory created when the AMOS distribution is untarred. Documentation on the examples is included with the distribution in /docs/minimus.README.

== Basic usage ==

To run minimus will you need a set of sequence files. Assuming you have a set of reads in fasta format called '''my_reads.seq''', you can run minimus with the following two commands:

toAmos -s my_reads.seq -o my_reads.afg

minimus my_reads

The output will be a fasta formatted file called '"my_reads.fasta"', a contig file with details about the assembly of each contig called '"my_reads.contig"', and an AMOS bank folder with various files used internally by minimus.
The toAmos file conversion utility is the most general and probably the most useful of the file conversion utilities included with minimus. More information about toAmos and the [[File_conversion_utilities | other file conversion utilities]] can be found in the [[AMOS | AMOS documentation wiki]]. For example, you can include quality data from a Phred style quality score file by running [[ToAmos | toAmos]] with the -q option as follows:

toAmos -s my_reads.fasta -q my_reads.qual -o asm_reads.afg

Minimus can also be called with the following equivalent command:

runAmos -C $AMOSBASE/src/Pipeline/minimus.acf asm_reads

The AMOS package also includes other helpful tools such as [[Hawkeye]], which is useful for evaluating your assembly with respect to paired-end reads. It can be run on the minimus bank with the following command:

hawkeye asm_reads.bnk/

== Publication ==

[http://www.biomedcentral.com/1471-2105/8/64 Minimus: a fast, lightweight genome assembler]

Sommer, DD, Delcher, AL, Salzberg, SL, and Pop, M. (2007) BMC Bioinformatics, 8:64doi:10.1186/1471-2105-8-64.

== Acknowledgements ==
The development of minimus was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS and by Department of Homeland Security cooperative agreement W81XWH-05-2-0051.

AMOS

2010-11-09T16:23:19Z

Decaos: Changes related to Nov 2010 AMOS release

{| align="right"
| __TOC__
|}

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.

Quick links:
* [[AMOS Getting Started]]
* [http://sourceforge.net/project/showfiles.php?group_id=134326 Download]
* [http://sourceforge.net/projects/amos SourceForge project page]

== Announcements ==

* November 10th, 2009 - New version of AMOS released!

== Documentation ==
Additional documentation in development through the [[AMOS Documentation Project]]

=== Assemblers ===
* [[ABBA]] - Assembly Boosted By Amino Acid Sequences
* [[AMOScmp]] - comparative assembler
* [[AMOScmp-shortReads]] - comparative assembler for short reads (Solexa,454)
* [[AMOScmp-shortReads-alignmentTrimmed]] - comparative assembler for short reads that uses alignment based trimming
* [[minimus]] - basic genome assembler for small datasets
* [[minimus2]] - basic genome assembler for two datasets; can also be used as an assembly merge pipeline
* [[minimo]] - the minimus assembler with many more options

=== Validation and Visualization ===
* [[Hawkeye]] - assembly viewer
* [[amosvalidate]] - assembly forensics
* [[Benchmark]] - assembly benchmark data

=== Scaffolding ===
* [[Bambus]] - Open source standalone hierarchical scaffolding
* [[Bambus2]] - Scaffolding Polymorphic Genomes and Metagenomes

=== Trimming, Overlapping, & Error Correction ===
* [[Figaro]] - statistical vector trimmer
* [[UMD Overlapper]] - High quality overlap computations
* [[KI Overlapper]] - Repeat aware overlapper
* [[AutoEditor]] - Automatic correction of genome sequencing errors
* [[FastqQC]] - Read composition and quality

=== Utilities ===
* [[File conversion utilities]] - converting data to and from AMOS
* [[AMOS Utilities | AMOS Utilities]] - general utilities
* [[runAmos]] - Pipeline executor

=== AMOS Development ===
* [[Programmer's guide]] - Getting started with the Source code
* [[Infrastructure]] - Developer level details
* [[Wiki guide]] - Guide for editing the wiki

=== Assembly Tutorials ===
* [http://www.cbcb.umd.edu/research/assembly_primer.shtml Assembly primer] - overview of genome assembly.
* [http://www.cbcb.umd.edu/research/contig_representation.shtml Representing assemblies (not just in AMOS)]
* [http://wgs-assembler.sourceforge.net Running Celera Assembler]

== Download ==
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.

[http://sourceforge.net/project/showfiles.php?group_id=134326 Download from SourceForge]

== Consortium members ==

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.

* University of Maryland, Center for Bioinformatics and Computational Biology
** project organization and direction
** infrastructure
** consensus
** automated sequence editing
** scaffolding
** overlap detection
** contig construction

* The Institute for Genomic Research
** production pipelines
** automated finishing tools
** error correction

* Karolinska Institutet
** overlap detection
** error correction

* Marine Biological Laboratory - Woods Hole
** graphical interface
** integration of assembly data with analysis (gene, polymorphism, etc.) information

== Join the consortium ==

All interested parties are welcome to join or aid the AMOS consortium. Please address all correspondence via Email to:

amos-help (at) lists (dot) sourceforge (dot) net

To receive information regarding new releases and developments, please subscribe to our moderated, low-traffic users' mailing list:

amos-users (at) lists (dot) sourceforge (dot) net

== Bug reports and support ==

For AMOS bug reports or support requests, please browse our SourceForge project page or Email us at:

amos-help (at) lists (dot) sourceforge (dot) net

== Acknowledgements ==

The AMOS consortium would like to thank the following organizations for their funding and/or support:
* The National Institutes of Health - grants R01-LM06845, N01-AI-15447
* The National Science Foundation - grants IIS-9902923, IIS-9820497
* Department of Homeland Security - cooperative agreement W81XWH-05-2-0051
* SourceForge.net