AMOScmp-shortReads: Comparative assembly pipeline for short reads

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
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
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)
Note: This pipeline has been introduced to the AMOS package starting with the release 2.0.8. If you have an older version of the AMOS package installed, it is highly recommended to upgrade it to the latest version.
 Alternatively, the new file could be manually downloaded and installed from the following location: AMOScmp-shortReads