What's a good PacBio CLR read simulator?
We could not use:
- SiLiCO source doesn't generate quality values
- FastqSim source has a bug where it outputs spurious A's and C's after 6 kbp
- SimLord source outputs only CCS reads
- pbsim source does not compile
- readsim source - No control on quality value, we tried to assemble 60x E.coli simulated reads and obtained very fragmented assemblies with Canu 1.4
We were able to use:
- LongIslnd source but is quite heavy-weight, it requires to install SMRTAnalysis (!) to generate model files. Model files aren't provided (this wasn't clear in the documentation), and it took over an hour to generate them myself. But helpful automated scripts were provided.
- BBMap's RandomReads source seems work, and easy to install (thanks to Brian Bushnell)
- NPBSS source MATLAB OCTAVE seems work but maybe not support multi-line FASTA.
Did you know other PacBio CLR read simulator ?
Edit : add BBmap's RandomReads and NPBSS