View source for AMOScmp-shortReads

== 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
* uses a smaller make-consensus alignment wiggle value


== Parameters ==

AMOScmp-shortReads allows for additional input parameters compared to AMOScmp.
Defaults:

   MINCLUSTER  = 20
   MINMATCH    = 20
   MINOVL      = 5
   MAXTRIM     = 10
   MAJORITY    = 50
   CONSERR     = 0.06
   ALIGNWIGGLE = 2


== How to run ==

Input files:
Assuming that prefix is the name of the organism to assemble, two files are required:

   1. prefix.1con : reference sequence: a related organism sequence in FASTA format (complete or well assembled, usually downloaded from GenBank)
   2. prefix.afg : AMOS message file that contains read/fragment messages corresponding to each short read; it can be generated using the toAmos script

Example:
   $ toAmos -s prefix.seq -o prefix.afg                           # create an AMOS message file from short read FASTA sequences
   $ AMOScmp-shortReads-alignmentTrimmed prefix                   # assemble reads (alignment based trimming, default parameters)