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  • A can of Worms - Which all purpose aligner to replace BWA 0.5.7 for Illumina data?

    Hi all,

    Currently in our pipeline we are using BWA 0.5.7 in at least a part of all types of illumina data analysis.

    By all types of data, I mean everything that comes off the sequencer. Mostly, this is limited to human sequence of any of the following types:
    RNA-seq: strand, or non, mate-pair or paired-end
    miRNA
    DNA: mate-pair, paired-end
    Chip

    I have listed mate-pair because we do it sometimes, but 99% all all the data are paired-end 2x150 reads.

    Since there are newer version of BWA, we're going to be evaluating them for our purposes, but since we're in the process of testing we are interested in hearing if anyone out there has recommendations for any other workhorse aligner. We can eliminate most aligners by saying they must be at least as fast as BWA to work (I suppose we're limiting to BWT aligners then?). We currently use samtools and picard for most post-alignment analysis.

    Has anyone recently upgraded their pipeline aligner from BWA 0.5.7 to something that has caused overall happiness in their organization? There of course are infinite ways to look at evaluating an aligner, so I am interesting in hearing from anyone who has used something newer on a variety of data types.

    All feedback is greatly appreciated!

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