Re: [Seqan-dev] Performance advice for whole genome ESA

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

Hi,

I've done some more reading ( http://trac.seqan.de/wiki/HowTo/EfficientImportOfMillionsOfSequences) and as far as I can tell I should just be using memory mapped files as a mechanism to read large sequence sets into main memory. Likewise this is the area where compression on disk could help. If I want to iterate over a ESA I'm best off copying the sequences into a standard seqan StringSet in main memory and creating the ESA on top of that. Please let me know if I've got the wrong end of the stick.

Regards,
John.

On 21/06/12 16:33, John Reid wrote:

Hi,

I'm reading the whole mouse genome into a seqan::IndexEsa based on a
seqan::StringSet. At the moment I have the genome (2,730,871,774 bp)
stored in one uncompressed fasta file on disk. Once I have the genome
loaded I'm iterating over it many times looking at all the words < about
20bp. I'm wondering if there is a better way to go about this. Should I
be looking at memory mapped files and/or compression on disk? Any
pointers or advice would be welcome.

Thanks,
John.

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