Replicating ELAND alignment using Bowtie2
I am attempting to replicate a workflow that used ELAND for alignment of reads. I don't have access to ELAND, but according to an article here,
Eland guarantees full sensitivity for hits with up to two mismatches
and ELAND
achieves full sensitivity given a threshold
is there a way to approximate this functionality in Bowtie2 by modifying some of the parameters? I see that there is a --very-sensitive argument, but I don't understand what level of sensitivity this targets, or for how many mismatches that sensitivity level is applicable.
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ELANDhas been deprecated for a decade. Any alignments you do with current aligners should be as good (or better) with default parameters. If you have the eland alignment available you can compare the stats on both.