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error/mismatch rate threshold for long-read alignment with GMAP or minimap2



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  • error/mismatch rate threshold for long-read alignment with GMAP or minimap2

    Hello all -- my bioinformatics experience is mostly with mapping Illumina reads (to mammalian transcriptomes) using STAR. But lately my group is starting to do more work with long-read sequencing, on both PacBio and Nanopore platforms, and I'm gradually getting familiar with how to map such data. So far I've been using either the GMAP or minimap2 aligners.

    My question is about setting an alignment threshold, in terms of a rate of errors (mismatches and/or indels) with respect to the genome reference. That is, I'd like to be able to limit the alignments I get to only those that have, say, a 95% exact match between the read and the reference, or only those reads with less than, say, 20 total mismatches.

    With STAR, this can be controlled via the Output Filter options, such as "--outFilterMismatchNoverLmax" or "--outFilterMatchNminOverLread". But I can't figure out if there is any equivalent or similar command-line parameter that can be used in GMAP or minimap2. Can anyone advise me on this?

    Thanks very much!

    STAR -- https://github.com/alexdobin/STAR/bl...STARmanual.pdf
    GMAP -- https://github.com/juliangehring/GMA.../master/README
    minimap2 -- https://github.com/lh3/minimap2

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