samtools: SAM (Sequence/Alignment Mapping) Tools

Contents

  1. Overview of package
  2. Overview of package
    1. General usage
  3. Availability of package by cluster

Overview of package

General information about package
Package: samtools
Description: SAM (Sequence/Alignment Mapping) Tools
For more information: http://www.htslib.org
Categories:
License: OpenSource (BSD, MIT)

General usage information

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

This module will add the samtools and related commands to your PATH.

In case you need to link against this library in your code, the following environmental variables have been defined:

  • \$SAMTOOLS_ROOT has been set to the root of the samtools installation
  • \$SAMTOOLS_LIBDIR points to the directory containing the libraries
  • \$SAMTOOLS_INCDIR points to the directory containing the header files

You will probably wish to use these by adding the following flags to your compilation command (e.g. to CFLAGS in your Makefile):

  • -I\$SAMTOOLS_INCDIR
and the following flags to your link command (e.g. LDFLAGS in your Makefile):
  • -L\$SAMTOOLS_LIBDIR -Wl,-rpath,\$SAMTOOLS_LIBDIR

Available versions of the package samtools, by cluster

This section lists the available versions of the package samtoolson the different clusters.

Available versions of samtools on the Deepthought2 cluster (RHEL8)

Available versions of samtools on the Deepthought2 cluster (RHEL8)
Version Module tags CPU(s) optimized for GPU ready?
1.10 samtools/1.10 ivybridge Y

Available versions of samtools on the Juggernaut cluster

Available versions of samtools on the Juggernaut cluster
Version Module tags CPU(s) optimized for GPU ready?
1.10 samtools/1.10 skylake_avx512, x86_64, zen Y