I've updated the BINSEQ manuscript to stay up to date with changes since I originally put it out at the beginning of the year Some notable changes: 1. Support for ambiguous bases with 4bit encoding 2. Support for sequence headers 3. Improved API biorxiv.org/content/10.1101/…

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences

Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput...

biorxiv.org

Oct 29, 2025 · 8:41 PM UTC

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I've also added some nice functionality to bqtools including a very useful colored grep! github.com/arcinstitute/bqto…

GitHub - ArcInstitute/bqtools: A command line utilty for working with BINSEQ files

A command line utilty for working with BINSEQ files - ArcInstitute/bqtools

github.com
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And if you're interested in building with binseq here is the place to start! github.com/arcinstitute/bins…

GitHub - ArcInstitute/binseq: A high efficiency binary format for sequencing data

A high efficiency binary format for sequencing data - ArcInstitute/binseq

github.com
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And stay on the look out the next couple weeks (hopefully) for the release of an even bigger project built with binseq!