I'd like to use novoalign for alignments since I've found it to be very accurate, but it is very slow at short read lengths.
Heng li stated elsewhere that Novo is 2-3X slower than BWA at 100bp reads, but ~10X slower for 40bp reads (http://seqanswers.com/forums/showpos...37&postcount=8)
I'm aligning 25bp reads and novo is impractical using the default settings. Any tips for tweaking it to increase speed?
Alternatively, what aligners people are using for outward facing reads, since BWA can only handle standard PE at this point?
Heng li stated elsewhere that Novo is 2-3X slower than BWA at 100bp reads, but ~10X slower for 40bp reads (http://seqanswers.com/forums/showpos...37&postcount=8)
I'm aligning 25bp reads and novo is impractical using the default settings. Any tips for tweaking it to increase speed?
Alternatively, what aligners people are using for outward facing reads, since BWA can only handle standard PE at this point?