[Seqan-dev] Performance advice for whole genome ESA

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

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.