bamtocov
March 20, 2026 ยท View on GitHub
Tools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.
:book: Documentation
Full documentation is available online at the :book: dedicated website, or in
this repository under docs.
Installation
The BamToCov package is available from :package: BioConda
conda install -y -c bioconda bamtocov
Benchmarks
Bamtocov has the smallest memory footprint of any other coverage tool, while maintaining reasonable speeds
- Four BAM files used for the benchmarks are available from Zenodo
- A Dockerfile with an automatic speed test is available in this repository
See also
- Brent Pedersen, Aaron Quinlan, hts-nim: scripting high-performance genomic analyses (Bioinformatics)
- Giovanni Birolo, Andrea Telatin, covtobed: a simple and fast tool to extract coverage tracks from BAM files (JOSS)
Initially we also used Lapper, and I recommend checking out this library for fast interval operations.
Cite
Giovanni Birolo, Andrea Telatin, BamToCov: an efficient toolkit for sequence coverage calculations, Bioinformatics, 2022