Software To Simulate Solid Colorspace Reads
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13.3 years ago
Travis ★ 2.8k

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.

simulation next-gen sequencing solid • 3.2k views
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13.3 years ago
Drio ▴ 920

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

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

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

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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.

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

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