http://amos.sourceforge.net/wiki/index.php?action=history&feed=atom&title=AMOScmp-shortReads 2026-04-30T04:33:20Z Revision history for this page on the wiki MediaWiki 1.23.5 http://amos.sourceforge.net/wiki/index.php?title=AMOScmp-shortReads&diff=50&oldid=prev 2009-07-07T20:40:08Z

<p>New page: == Overview == AMOScmp-shortReads is a modified version of AMOScmp designed for assembling short reads. Differences compared to AMOScmp: * uses a smaller nucmer alignment cluster size * u...</p> <p><b>New page</b></p><div>== Overview ==<br /> <br /> AMOScmp-shortReads is a modified version of AMOScmp designed for assembling short reads.<br /> Differences compared to AMOScmp:<br /> * uses a smaller nucmer alignment cluster size<br /> * uses a smaller make-consensus alignment wiggle value<br /> <br /> <br /> == Parameters ==<br /> <br /> AMOScmp-shortReads allows for additional input parameters compared to AMOScmp.<br /> Defaults:<br /> <br /> MINCLUSTER = 20<br /> MINMATCH = 20<br /> MINOVL = 5<br /> MAXTRIM = 10<br /> MAJORITY = 50<br /> CONSERR = 0.06<br /> ALIGNWIGGLE = 2<br /> <br /> <br /> == How to run ==<br /> <br /> Input files:<br /> Assuming that prefix is the name of the organism to assemble, two files are required:<br /> <br /> 1. prefix.1con : reference sequence: a related organism sequence in FASTA format (complete or well assembled, usually downloaded from GenBank)<br /> 2. prefix.afg : AMOS message file that contains read/fragment messages corresponding to each short read; it can be generated using the toAmos script<br /> <br /> Example:<br /> $ toAmos -s prefix.seq -o prefix.afg # create an AMOS message file from short read FASTA sequences<br /> $ AMOScmp-shortReads-alignmentTrimmed prefix # assemble reads (alignment based trimming, default parameters)</div>

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