3 ms·
But see: http://snap.cs.berkeley.edu http://snap.cs.berkeley.edu. BWT-based aligners hark back to a time when it was not cheap to own enough RAM to store an ent
by hyperbovine 13y ago
But see: http://snap.cs.berkeley.edu http://snap.cs.berkeley.edu. BWT-based aligners hark back to a time when it was not cheap to own enough RAM to store an entire (human) genome seed lookup table in memory. That is no longer the case (you need about 64gb). Also, hash aligners perform better as the read length increases.
- epistasis 13y agoWell, BLAT for example also stores the entire seed table in memory, it just has to use fewer, shorter, and more frequently-occurring seeds. BWT requires something like two random RAM accesses per base pair, which is incredibly slow. With a large enough seed table, hash-based can get down to just a few random accesses per 100 base pair read. Has SNAP been published? I had heard about it but not seen it used in practice anywhere.
- epistasis 13y agoBTW, thank you for the pointer to the repository! I hadn't realized that it was publicly available at all. There's a few niceties that would be good, such as reading gzip directly (named pipes are a hassle). But also very cool that they're using HugeTLB, I'm always glad when good systems people apply themselves to bioinformatics, they can really squeeze the most out of recent machines!