BINSEQ

Overview

BINSEQ is a binary file format family for efficient storage and processing of DNA sequences. It uses two-bit encoding for nucleotides and is optimized for high-performance parallel processing.

The recommended variant is CBQ (*.cbq): a columnar, block-compressed format for variable-length records with optional quality scores and headers. It is lossless by default (native N support), compresses well, and decodes fast. For details on its structure see the documentation.

Two earlier variants remain supported:

• BQ (*.bq): fixed-length records without quality scores. Minimal and fast for uniform reads.
• VBQ (*.vbq): variable-length records with optional quality scores and headers. Superseded by CBQ, which improves on its compression and decoding speed; new projects should use CBQ.

All variants support both single and paired sequences.

Getting Started

This is a library for reading and writing BINSEQ files; for a command-line interface see bqtools.

To get started please refer to our documentation. For example programs which make use of the library check out our examples directory.

For more information about the BINSEQ file family, please refer to our preprint.