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

This page summarizes the projects mentioned and recommended in the original post on reddit.com/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.

  • Scout APM

    Less time debugging, more time building. Scout APM allows you to find and fix performance issues with no hassle. Now with error monitoring and external services monitoring, Scout is a developer's best friend when it comes to application development.

  • 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

    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

    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.

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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