Sambamba

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

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.

Binaries

If you are already a Conda user, please use bioconda channel. If you are not, strongly consider becoming one.

Users of Homebrew can also use the formula from homebrew-science.

For those not in the mood to learn/install new package managers, there are of course Github releases.

Compiling Sambamba

The preferred method for compiling Sambamba is with the LDC compiler which targets LLVM.

Compiling for Linux

The LDC compiler's github repository also provides binary images. The current preferred release for sambamba is LDC - the LLVM D compiler (>= 0.16.1). After installing LDC:

    git clone --recursive https://github.com/lomereiter/sambamba.git
    cd sambamba
    make sambamba-ldmd2-64

Installing LDC only means unpacking an archive and setting some environmental variables, e.g. unpacking into $HOME:

cd
wget https://github.com/ldc-developers/ldc/releases/download/v0.17.1/ldc2-0.17.1-linux-x86_64.tar.xz
tar xJf ldc2-0.17.1-linux-x86_64.tar.xz
export PATH=~/ldc2-0.17.1-linux-x86_64/bin/:$PATH
export LIBRARY_PATH=~/ldc2-0.17.1-linux-x86_64/lib/

Compiling for Mac OS X

    brew install ldc
    git clone --recursive https://github.com/lomereiter/sambamba.git
    cd sambamba
    make sambamba-ldmd2-64

Troubleshooting

In case of crashes it's helpful to have GDB stacktraces (bt command).

Note that GDB should be made aware of D garbage collector:

handle SIGUSR1 nostop
handle SIGUSR1 noprint
handle SIGUSR2 nostop
handle SIGUSR2 noprint

Development

Sambamba development and issue tracker is on github. Developer documentation can be found in the source code and the development documentation.

Copyright

Sambamba is distributed under GNU Public License v2+.

Citation

If you are using Sambamba in your research, please cite the following article:

A. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. Sambamba: fast processing of NGS alignment formats. Bioinformatics, 2015.

itsjeffreyy / sambamba