How to split a whole genome sequence file?

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9.7 years ago

fashiondesignrussian ▴ 60

How to split a whole genome sequence file (see also here)? I have 8 GB RAM and my computer chokes with large whole genome sequence .gb and fasta files. Please tell how to split the file and advise a software which can do alignment fast with low memory requirements. I have tried Geneous Pro, CLS Genomics, DNA Star, SeqSphere --- all need at least 16-32 RAM.

sequencing next-gen wgs • 3.2k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by fashiondesignrussian ▴ 60

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Split them according to what?

ADD REPLY • link 9.7 years ago by Devon Ryan 104k

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Splitting the file should not be a problem (depending on how you wanna split it) the simplest way is to pick a sliding window size and print everything what is in it, to different files. (Let me know if there is a need for a simple parser do do this or you can manage on your own). As far as the software tool goes, these tools are not designed to run with low memory requirements. Usually they are in memory algorithms. Now depending on what you are trying to achieve, there is a chance for you to get away with splitting the input file, but in order for me to give some advice I would need more information.

cheers
mxs

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by mxs ▴ 530

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