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  • bwa-mem2

    The next version of bwa-mem

    I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true).

  • htslib

    C library for high-throughput sequencing data formats

    Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly.

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NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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