http://amos.sourceforge.net/wiki/index.php?action=history&feed=atom&title=AMOScmp 2026-04-30T08:12:29Z Revision history for this page on the wiki MediaWiki 1.23.5 http://amos.sourceforge.net/wiki/index.php?title=AMOScmp&diff=49&oldid=prev 2009-07-07T20:38:51Z

<p>New page: == 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 compa...</p> <p><b>New page</b></p><div>== Overview ==<br /> <br /> 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.<br /> <br /> <br /> AMOScmp is composed of 3 main modules:<br /> * [[MUMmer]]: align reads to reference<br /> * [[casm-layout]]: analyze alignments and build contig layouts<br /> * [[make-consensus]]: generate contig consensus<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 /> == Related Tools ==<br /> <br /> * [[AMOScmp-shortReads]] is a modified version AMOScmp designed for assembling short reads.<br /> <br /> * [[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.<br /> <br /> <br /> <br /> == Documentation ==<br /> <br /> Documentation on running AMOScmp is included with the distribution in the /docs subdirectory.<br /> <br /> <br /> == References ==<br /> <br /> &quot;Comparative Genome Assembly.&quot; Pop M, Phillippy A, Delcher AL, Salzberg SL, Briefings in Bioinformatics, 2004. 5(3):237-48.<br /> <br /> <br /> == Acknowledgements ==<br /> The development of AMOScmp was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS.</div>

Mcschatz