Question

Software To Simulate Solid Colorspace Reads

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12.8 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 • 3.0k views

ADD COMMENT • link updated 12.1 years ago by Drio ▴ 920 • written 12.8 years ago by Travis ★ 2.8k

score 1 · Answer 1 · 2011-07-22

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12.8 years ago

Drio ▴ 920

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

ADD COMMENT • link 12.8 years ago by Drio ▴ 920

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

ADD REPLY • link 12.7 years ago by Travis ★ 2.8k

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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

ADD REPLY • link 12.7 years ago by Ian 6.0k

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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.