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Generate artificial reads

Hello,

i need to generate some artifical reads. randomsreads.sh from BBMap seems to be the right program for me.

I don't need random reads for my whole reference genome but for several thousand regions. So I wonder if there is better/faster way instead of first creating a separate ref file for every region? Maybe a new parameter for randomreads.sh for providing a bed file with the region (@Brian Bushnell :) )

fin swimmer

bbmap fastq randomreads
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updated by Joe Joe • written by finswimmer finswimmer

2 answers

You can do this with bedtools and wgsim:

# Generate FASTA file of regions    
bedtools getfasta -fi reference.fasta -bed regions.bed > regions.fasta

# Generate reads from FASTA file of regions
wgsim regions.fasta reads_1.fastq reads_2.fastq
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written by James Ashmore James Ashmore

Why not go back to randomreads.sh after bedtools getfasta. OP is happy with it otherwise :-)

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written by GenoMax GenoMax

Good point, I'm not familiar with BBMap, either will work I guess

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written by James Ashmore James Ashmore

The combination with bedtools getfasta and randomreads.sh works perfect.

Thank you all.

fin swimmer

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written by finswimmer finswimmer

Haven't tried it personally, but ART is used a lot in my lab for this:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762/

Not sure if it will do a region-by-region thing, though you could probably simulate a genome and then work backwards throwing away the uncessary stuff with bedtools or similar.

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written by Joe Joe

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