Replicating ELAND alignment using Bowtie2
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6.0 years ago
jacobcvt12 • 0

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.

alignment • 860 views
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ELAND has 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.

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