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AMOScmp: Comparative assembly package |
Overview
A comparative assembler is a program that can assemble a set of shotgun reads from an organism by mapping them to the finished sequence of a related organism. Thus, a comparative assembler transforms the traditional overlap-layout-consensus approach to alignment-layout-consensus. The AMOScmp package uses the MUMmer program to perform a mapping of the reads to the reference genome, then processes the alignment results with a sophisticated layout program designed to take into account polymorphisms between the two genomes. For a detailed description of the algorithms involved please refer to the paper listed in the References section.
AMOScmp uses as AMOS messages as both the inputs and the outputs (see documentation). Two utilities are provided to process these files: tarchive2amos - a versatile converter from trace archive .seq, .qual, and .xml information into AMOS formatted data; amos2ace - a converter from AMOS formatted data to the .ACE assembly format. In addition, the AMOS::AmosLib Perl module is provided as a tool for users who prefer to write their own conversion utilities. Please see the documentation included with the distribution for more information.
AMOScmp is part of the AMOS package - a collaborative effort to develop a modular open-source framework for assembly development.
AMOScmp-shortReads is a modified version AMOScmp tuned for assembling short reads
AMOScmp-shortReads-alignmentTrimmed: same as AMOScmp-shortReads but the reads are trimmed based on their alignment to a reference sequence
System requirements
AMOScmp consists of a collection of C/C++ and Perl modules running under Unix. In order to compile and run AMOScmp you must first install the MUMmer package. The Perl components rely on Perl 5.6.0 or later. You can obtain a current version of Perl from CPAN if one is not already installed on your system. The C/C++ components have been tested under gcc 2.9x and 3.x on Linux RedHat 7.3, Mac OSX, and OSF1 V5.1. We expect the code will compile with minimal changes on any other Unix-based operating system.
Obtaining AMOScmp
This software is OSI
Certified Open Source Software.
Documentation
Compiling minimus involves the following steps:
- Unpack the AMOS distribution:
gzip -dc amos-<version>.tar.gz | tar -xf -
(replace <version> with the current version of the distribution. - Change directories to the top level of the distribution:
cd amos-<version> - Run the configuration script that identifies the specific configuration
of your system.
./configure --disable-all --enable-AMOScmp
At this step you may also specify the location where you want the code to be ultimately installed:
./configure --disable-all --enable-AMOScmp --prefix=/usr/local/
By default the code will be installed in the directory from which you ran theconfigurecommand - Compile the code
make all - Install the binaries in the appropriate locations
make install
Documentation on running AMOScmp is included with the distribution in
the /docs subdirectory.
Contact Information
You can contact us at:
References
"Comparative Genome Assembly." Pop M, Phillippy A, Delcher AL, Salzberg SL, Briefings in Bioinformatics, 2004. 5(3):237-48.