sqzlib - kseq compatible DNA fastA/Q encoding and compression library

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics

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  • sqzlib

    Blocked bases fastX encoding and compression

  • Klib

    A standalone and lightweight C library

    Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.

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  • seqstats

    Quick summary statistics on fasta/fastq(.gz) files

    Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.

  • minimap2

    A versatile pairwise aligner for genomic and spliced nucleotide sequences (by 7PintsOfCherryGarcia)

    Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.

  • bwa-mem2

    The next version of bwa-mem (by 7PintsOfCherryGarcia)

    Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.

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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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