VelvetK

Description

VelvetK can estimate the best k-mer size to use for your Velvet de novo assembly. It needs two inputs: the estimated genome size, and all your sequence read files. The genome size can be supplied as as a number (eg. 3.5M) or as a FASTA file of a closely related genome. The reads can be FASTA or FASTQ, and may optionally be compressed with GZIP or BZIP2.

Download

velvetk.pl - 6 June 2012

Screenshot

Synopsis:
  List suitable k-mer sizes given target genome and reads
Author:
  Torsten Seemann (torsten@seemann.id.au)
Usage:
  velvetk.pl [--size X | --genome F] [options] <readfile[.gz][.bz2] ...>
Options:
  --help          This help.
  --verbose!      Verbose output (default '0').
  --size=s        Target genome size in bp (can use k/M/G suffix) (default '0').
  --genome=s      Target genome (FASTA) (default '').
  --cov=i         Target k-mer coverage (default '25').
  --range=i       Print target +/- this range (default '10').
  --best!         Just print best k-mer to stdout (default '0').

License

GPL v2

Requirements

Perl >= 5.6

Contact

Torsten Seemann