I want to generate reads from a set of different haplotype sequences found at different frequencies within a sample. I was wondering whether any Biostar users had any experience of doing this and which tools they used. I would prefer using an existing tool but there are quite few out there (I have compiled some in the table below). I am wondering which one will suit my purpose best.
Any advice is very welcome - thanks.
|Name||Reference||Single-end||Paired-end||insert size between reads||Quality score||customise read length||coverage bias||Phred score from existing FASTQ||Simulated sequencing errors||insertion-deletion errors||source||platforms|
|ArtificialFastqGenerator||doi: 10.1371/journal.pone.0049110||yes||yes||yes||yes||yes based on GC||yes||yes||https://sourceforge.net/projects/artfastqgen/||illumina|
|ART||doi: 10.1093/bioinformatics/btr708||yes||yes||no||yes||yes||yes||yes||Roche 454, Illumina Solexa, Applied Biosystem SOLiD|
|WgSim||doi: 10.1093/bioinformatics/btp352||dummy quality scores||uniform distribution error||yes by simulating INDEL polymorphisms|
|Mason||Holtgrewe M (2010) Mason - a read simulator for second generation sequencing data. Technical report, FU Berlin.||yes||yes||yes||no||yes||random||454, Illumina, Sanger|
|SimSeq||Available: https://github.com/jstjohn/SimSeq. Accessed 2012 October 10th.||yes||yes||yes||<100bp||Illumina|
|pIRS||doi: 10.1093/bioinformatics/bts187||yes||empirical model based on read cycle||yes based on GC||empirical model based on read cycle||yes with additional tool|