HTSlib - C library for reading/writing high-throughput sequencing data

  1. James K. Bonfield
  2. John Marshall
  3. Petr Danecek
  4. Heng Li
  5. Valeriu Ohan
  6. Andrew Whitwham
  7. Thomas Keane
  8. Robert M. Davies

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Abstract

Background

Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.

Findings

We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.

Conclusion

Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19).

Widespread adoption has seen HTSlib downloaded over a million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT / BSD license.

Contact

samtools@sanger.ac.uk

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giab007

    James K. Bonfield 1Wellcome Trust Sanger Institute Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for James K. BonfieldJohn Marshall 2University of Glasgow, Institute of Cancer SciencesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for John MarshallPetr Danecek 1Wellcome Trust Sanger Institute Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Petr DanecekHeng Li 3Dana-Farber Cancer Institute and Harvard UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Heng LiValeriu Ohan 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Valeriu OhanAndrew Whitwham 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrew WhitwhamFor correspondence: aw7@sanger.ac.ukThomas Keane 5EMBL-EBIFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas KeaneRobert M. Davies 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert M. Davies

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab007 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102657 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102658

  2. Version published to 10.1101/2020.12.16.423064v2 on bioRxiv
  3. Version published to 10.1093/gigascience/giab007
  4. Version published to 10.1101/2020.12.16.423064v1 on bioRxiv