Home

ReadSim

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

Manual

---

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) ***