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 is composed of 3 main modules:
- MUMmer: align reads to reference
- casm-layout: analyze alignments and build contig layouts
- make-consensus: generate contig consensus
For additional information on short read assembly check the following University of Maryland CBCB web sites:
- AMOScmp-shortReads is a modified version AMOScmp designed for assembling short reads.
- AMOScmp-shortReads-alignmentTrimmed is a modified version AMOScmp designed for assembling short reads. Reads get trimmed based on their alignment to a reference sequence prior to alignment.
Documentation on running AMOScmp is included with the distribution in the /docs subdirectory.
"Comparative Genome Assembly." Pop M, Phillippy A, Delcher AL, Salzberg SL, Briefings in Bioinformatics, 2004. 5(3):237-48.
The development of AMOScmp was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS.