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
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/stdout as filenames.
samtools implements parallel BAM compression in
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.
See Github releases.
Users of Homebrew are advised to use the formula from
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 (0.14.0). After installing LDC:
git clone --recursive https://github.com/lomereiter/sambamba.git cd sambamba make sambamba-ldmd2-64
Compiling for Mac OS X
brew install ldc git clone --recursive https://github.com/lomereiter/sambamba.git cd sambamba make sambamba-ldmd2-64
Compiling for Linux using Docker
Use the Docker image which contains all binaries necessary for compilation:
docker pull lomereiter/centos-ldc docker run -i -t lomereiter/centos-ldc /bin/bash $ git clone --recursive https://github.com/lomereiter/sambamba.git $ cd sambamba && make sambamba-ldmd2-64 $ ^D docker cp `docker ps -l -q`:/sambamba/build/sambamba /usr/local/bin/
Sambamba is distributed under GNU Public License v2+.