Software To Simulate Solid Colorspace Reads

Question

[Travis]

Is anyone aware of software that will generate simulated colorspace reads?

wgsim is supposed to do it but the functionality does not seem to work - I an only get standard fastq data as output.

Thanks in advance.

Answer 1

[Drio]

Dnaa will do it. Use dnaa/dwgsim/dwgsim within the package.

[Travis]

It doesn't work. Whilst it has the option to output colorspace data (-c), the output is still fastq.

[Ian]

Here is a method from Seqanswers (from Nils Homer) that converts FASTQ to .csfasta and .qual: http://seqanswers.com/forums/showthread.php?t=2360

[Travis]

Shouldn't a .csfasta file contain numbers instead of letters? Nils' script only separates the sequence and quality information and converts the quality scores so far as I can see.

[Drio]

Do you enable the -c flag to tell the tool to generate reads in color space?