Any state of the art tool for reads generation from reference sequence?

Question

[Alex]

Dear Biostar Community,

What is the best tool for read generation from given reference sequences or any that you use/used and it works/worked as expected?

The properties of desired tool:

• reads generate of given insert size and read length with uniform coverage
• handle uniform coverage on circle genomes
• handle large genomes without crashing
• generation of Illumina reads
• generation of PacBio reads
• generation of reads without errors
• generation of reads contaminated by technical sequences
• generation of read-through adapters artefacts

I used ART (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/) but it looks like it uses too old model for Illumina.

[James Ashmore]

Possibly wgsim, although it only has a few of the features you require.

[russell]

Ditto with Sherman, but maybe worth a look

Answer 1

[GenoMax]

randomreads from BBMap.
PacBio reads can be generated this way.

[harold.smith.tarheel]

+1 for BBMap's randomreads, and it offers the additional bonus that the developer, Brian Bushnell, is very responsive if you need help.