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ReadSim

ReadSim is a fast and simple reads simulator to target long reads such as PacBio or Nanopore.

Manual

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Release Notes

ReadSim v1.6 (Nov, 21, 2014)

• dnasim.py is added.
  • dnasim.py simulates heterozygous polyploidy genome.
  • ./dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
• pacbio.p5-c3.len.dist file is included.
  • You can use it as a parameter of '--read_dist'.
  • ./readsim.py sim fq --ref hg19.chr1.fa --pre chr1.c10 --rev_strd off --replace yes --tech pacbio --cov_mu 10 --read_dist pacbio.p5-c3.len.dist
  • This will provide more realistic simulation than {uniform, normal, exp} distribution.
• Faster!!! Speed is improved
  • A 4-day job takes only 2 hours!!!
• timestamp is added

ReadSim v1.5 (Jan, 16, 2013)

• Make simulated reads more realistic
  • The option '--read_dist' can take a file, in which each line has a length of a read. File name cannot be {uniform, normal, exp}
  • ./readsim.py sim fq --ref hg19.chr1.fa --pre chr1.c10 --rev_strd off --replace yes --tech perfect --cov_mu 10 --read_dist lens.txt

ReadSim v1.4 (Dec, 3, 2012)

• Counting forward/backward reads are added.
  • (e.g) Total 70593 reads are generated; 40593 is forward, 30000 is reversed

ReadSim v1.3 (Dec, 3, 2012)

• reversed strands can be generated.
  • --rev_strd : on | off, 'on' means create backward strands as well as forward strands, randomly half and half. 'off' means no backward strands, every read is forward strand.

ReadSim v1.2 (Nov, 16, 2012)

ReadSim v1.1 (Nov, 13, 2012)

ReadSim v1.0 (Nov, 6, 2012)