gjospin/PhyloSift — Issue #120: Use lastal instead of bowtie2 for rna search of long seqs
Author: koadman
Created: 2012-03-06 06:15:58+00:00
State: open

bowtie2 requires many GB of memory to search seqs > 1Mb long and this can throw linux systems into fits.

lastal can do the same searches with reasonable memory usage.

This can be implemented as another search process and the octopus can hand out long seqs to lastal instead of bowtie2