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Old 03-30-2011, 01:40 AM   #1
schönblick
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Default recommend a short reads simulator?

can any one recommend a short reads (illumina) simulator?
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Old 03-30-2011, 02:07 AM   #2
jts
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I use SimSeq by John St. John:

https://github.com/jstjohn/SimSeq
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Old 03-30-2011, 02:54 AM   #3
steven
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You may want to try the Flux Simulator too
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Old 03-30-2011, 05:49 AM   #4
suryasaha
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Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.

Code:
Program: wgsim (short read simulator)
Version: 0.2.3
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>

Options: -e FLOAT      base error rate [0.020]
         -d INT        outer distance between the two ends [500]
         -s INT        standard deviation [50]
         -N INT        number of read pairs [1000000]
         -1 INT        length of the first read [70]
         -2 INT        length of the second read [70]
         -r FLOAT      rate of mutations [0.0010]
         -R FLOAT      fraction of indels [0.10]
         -X FLOAT      probability an indel is extended [0.30]
         -c            generate reads in color space (SOLiD reads)
         -C            show mismatch info in comment rather than read name
         -h            haplotype mode

Note: For SOLiD reads, the first read is F3 and the second is R3.
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Old 03-30-2011, 06:45 AM   #5
schönblick
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thanks all for suggestions!
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Old 09-20-2012, 09:06 AM   #6
mdk308
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Quote:
Originally Posted by suryasaha View Post
Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.
any idea how wgsim handles multifasta files? do i need to remove all of the headers or can i just run as is?
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Old 09-20-2012, 09:39 AM   #7
lyz1030
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can anyone tell me how wgsim simulate variants (the position can be specified ) or we can get the variant position. The objective is to evaluate the false negative rate of variant calling softwares.
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