cjfields/sambamba

Tools for working with SAM/BAM data (development suspended until July)

Sambamba

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with BAM files. Current functionality is an important subset of samtools functionality.

Because of efficient use of modern multicore CPUs, usually sambamba is much faster than samtools. For example, indexing a 2.5 Gb BAM file (fully cached into RAM) on a 8 core machine utilizes all cores at 64% CPU:

time sambamba index merged_NIT20120138_F3_20130715.bam -t8

  real    0m17.398s
  user    1m25.841s
  sys     0m3.752s

meanwhile samtools is 4x slower:

time samtools index merged_NIT20120138_F3_20130715.bam
  real    1m8.083s
  user    1m6.640s
  sys     0m1.448s

In practice, the speedup is usually smaller since I/O becomes a bottleneck. Even so, it makes a big difference, shifting the focus to I/O optimization, i.e. less temporary files, more UNIX pipes, faster disk storage, tweaking filesystem, etc. Most tools in sambamba support piping: just specify /dev/stdin or /dev/stdout as filenames.

Notice that samtools implements parallel BAM compression in sort and merge, but sambamba should be faster for these tasks (given same amount of memory) due to more cache-friendly approach to parallelization. If it is not the case for you, please file a bug.

Sambamba is free and open source software, licensed under GPLv2+. See manual pages online to know more about what is available and how to use it.

For more information on Sambamba you can contact Artem Tarasov and Pjotr Prins.

Quick install from source

Download LDC2 compiler from Github: https://github.com/ldc-developers/ldc/releases Add it to $PATH, fetch sambamba sources and run make, e.g. for Linux 64-bit:

wget https://github.com/ldc-developers/ldc/releases/download/v0.12.0/ldc2-0.12.0-linux-x86_64.tar.xz
tar xJf ldc2-0.12.0-linux-x86_64.tar.xz
git clone --recursive https://github.com/lomereiter/sambamba.git
cd sambamba
export PATH=../ldc2-0.12.0-linux-x86_64/bin:$PATH
make sambamba-ldmd2-64

The binary will be in build/ subdirectory.

Binaries

See Github releases

Note

If you are going to build LDC compiler from source, add -O3 flag in build/runtime/CMakeFiles/phobos-ldc.dir/flags.make when building LDC, otherwise Zlib library will be compiled without optimizations.

Copyright

Sambamba is distributed under GNU Public License v2+.