BINSEQ is a file format for storing nucleotide sequences as binary data. It is designed to be efficient and compact, making it suitable for large-scale genomic data analysis.

It has some benefits that make it an ergonomic choice for working with genomic data:

• Excellent compression of data
• Efficient parallel processing with random-access to records
• Paired records available in a single file (no separate R1/R2)

Our goal in this tutorial is to demonstrate how to use bqtools, a command-line tool that provides a set of utilities for working with BINSEQ files in the spirit of Unix utilities and other bioinformatics tools like samtools and bedtools.

We will cover the basics of importing/exporting sequencing data into BINSEQ files as well as some useful and common operations that can be performed with bqtools such as counting records, concatenation, and sequence grep.

For some more information about BINSEQ, its features, specifications, and how it compares to other formats, check out the BINSEQ preprint.

For more complete information about bqtools, check out its documentation

For programmatic access to BINSEQ, check out the BINSEQ rust docs.