can any one recommend a short reads (illumina) simulator?
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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 <[email protected]> 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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