in silico fragmentation of reads

[incognitos]

Hi,

I have read sequences that are 300 bases long (assembled from paired end 150b). I would like to create "fake reads" from the assembled sequence by randomly breaking up the reads to 50-60 base fragments and generate a few hundred reads in this in silico manner.

Does anyone know of a software that I could use to achieve this?

[Brian Bushnell]

Using the BBMap package, you can do this randomly with randomreads.sh or deterministically with shred.sh:

reformat.sh in=reads.fq out=reads.fasta
randomreads.sh ref=reads.fasta out=synth.fq minlen=50 maxlen=60 reads=500 adderrors=false

or

shred.sh in=reads.fastq out=shreds.fastq length=60 minlength=50 overlap=0 reads=500