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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:

  MINMATCH    = 20
  MINOVL      = 5
  MAXTRIM     = 10
  MAJORITY    = 50
  CONSERR     = 0.06

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


  $ 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)
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