Home 9 Resources 9 Software 9 HTSLIB


HTSlib is a C library for reading and writing high-throughput sequencing data.  It is the core library used by SAMtools and BCFTools.


  • HTSlib GitHub page
  • Citation: Please cite this paper when using HTSlib for your publications.

    HTSlib: C library for reading/writing high-throughput sequencing data
    James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M Davies
    GigaScience, Volume 10, Issue 2, February 2021, giab007, https://doi.org/10.1093/gigascience/giab007

Usage on Bridges-2

To see what versions of HTSlib are available and if there is more than one, which is the default, along with some help, type

module spider htslib

To use HTSlib, include a command like this in your batch script or interactive session to load the HTSlib module: (note ‘module load’ is case-sensitive):

module load htslib