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Pjotr Prins a4b00af81f
Merge pull request #420 from mschilli87/patch-1
9 months ago
.github Update 3 years ago
BioD @ 7969eb0a84 Adding benchmark for markdup 10 months ago
contrib/shunit2-2.0.3 shunit2: add sources in tree for unit testing 2 years ago
cram Updated Sambamba to use the latest BioD version - many modules got moved around. 1 year ago
deb fix #79; bump version 6 years ago
doc notes 1 year ago
etc/bash_completion.d ditto 6 years ago
htslib @ 2f3c3ea7b3 update to latest htslib 5 years ago
lz4 @ b3692db46d Reintroducing lz4 because Debian recently dropped lz4frames.h and related 2 years ago
man fix formatting 3 years ago
sambamba make error message more informative 1 year ago
scripts Always use Python 3+ 9 months ago
test Always use Python 3+ 9 months ago
thirdparty improved sort performance (needs testing) 6 years ago
utils Fixed Makefile.guix for development. Moved VERSION into its own file 1 year ago
.gitignore Add Meson build definition 9 months ago
.gitmodules Removing undeaD 1 year ago
.travis.yml Travis: fixing tests on Linux 2 years ago
.travis.yml.macos Travis: disable for now 2 years ago Fix GNU Guix install instructions 9 months ago
LICENSE license under GPL v2+ 8 years ago
Makefile Adding benchmark for markdup 10 months ago
Makefile.docker Makefile for LDC Docker images 2 years ago
Makefile.guix Building with Debian ldc2 10 months ago
Makefile.old Updated Make instructions and simplified the main Makefile. The following should work 2 years ago Badge 10 months ago Release notes added 10 months ago
VERSION Version bump in preparation for a release 10 months ago
dub.json dub: dropped dependency on undead 1 year ago Always use Python 3+ 9 months ago Add Meson build definition 9 months ago
meson_options.txt Add Meson build definition 9 months ago Use version in binary name 1 year ago
sambamba-ldmd-debug.rsp Save version strings from build chain and display in usage 3 years ago
sambamba-ldmd-release.rsp Makefile: fixed standard make file to support Dlang ./undeaD lib 3 years ago

Build Status AnacondaBadge DL [AnacondaVersion] BrewBadge GuixBadge DebianBadge


Table of Contents


Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency Sambamba is an important work horse running in many sequencing centres around the world today. As of November 2019, Sambamba has been cited over 277 times and has been installed from Conda over 120K times.

Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Most tools support piping: just specify /dev/stdin or /dev/stdout as filenames. When we started writing sambamba (in 2012) the main advantage over samtools was parallelized BAM reading and writing. In March 2017 samtools 1.4 was released, reaching parity at least on architecture. A recent performance comparison shows that sambamba still holds its ground and can even do better. Here are some comparison metrics. For example, for flagstat sambamba is 1.4x faster than samtools. For index they are similar. For Markdup almost 6x faster and for view 4x faster. For sort sambamba has been beaten, though sambamba is notably up to 2x faster than samtools on large RAM machines (120GB+).

In addition sambamba has a few interesting features to offer, in particular

  • fast large machine sort, see performance
  • automatic index creation when writing any coordinate-sorted file
  • view -L <bed file> utilizes BAM index to skip unrelated chunks
  • depth allows to measure base, sliding window, or region coverages
    • Chanjo builds upon this and gets you to exon/gene levels of abstraction
  • markdup, a fast implementation of Picard algorithm
  • slice quickly extracts a region into a new file, tweaking only first/last chunks
  • and more (you’ll have to try)

Even though Sambamba started out as a samtools clone we are now in the process of adding new functionality - also in the BioD project. The D language is extremely suitable for high performance computing (HPC). At this point we think that the BAM format is here to stay for processing sequencing data and we aim to make it easy to parse and process BAM files.

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 contact the mailing list (see Getting help).

Binary installation

Install stable release

For those not in the mood to learn/install new package managers, there are Github source and binary releases. Simply download the tarball, unpack it and run it according to the accompanying release notes.

Below package managers Conda, GNU Guix, Debian and Homebrew also provide recent binary installs for Linux. For MacOS you may use Conda or Homebrew.

Bioconda install

Install with CONDA

Ther should be binary downloads for Linux and MacOS.

With Conda use the bioconda channel.

GNU Guix install


A reproducible GNU Guix package for sambamba is available. The development version is packaged here.

Debian GNU/Linux install


See also Debian package status.

Homebrew install


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

brew install brewsci/bio/sambamba

It should work for Linux and MacOS.

Getting help

Sambamba has a mailing list for installation help and general discussion.

Reporting a sambamba bug or issue

Before posting an issue search the issue tracker and mailing list first. It is likely someone may have encountered something similar. Also try running the latest version of sambamba to make sure it has not been fixed already. Support/installation questions should be aimed at the mailing list. The issue tracker is for development issues around the software itself. When reporting an issue include the output of the program and the contents of the output directory.

Check list:

To find bugs the sambamba software developers may ask to install a development version of the software. They may also ask you for your data and will treat it confidentially. Please always remember that sambamba is written and maintained by volunteers with good intentions. Our time is valuable too. By helping us as much as possible we can provide this tool for everyone to use.

Code of conduct

By using sambamba and communicating with its communtity you implicitely agree to abide by the code of conduct as published by the Software Carpentry initiative.

Compiling Sambamba

Note: in general there is no need to compile sambamba. You can use a recent binary install as listed above.

The preferred method for compiling Sambamba is with the LDC compiler which targets LLVM. LLVM versions 6 is faster than earlier editions.

Compilation dependencies


Compiling for Linux

The LDC compiler’s github repository provides binary images. The current preferred release for sambamba is LDC - the LLVM D compiler (>= 1.6.1). After installing LDC from with, for example

tar xvJf ldc2-1.7.0-linux-x86_64.tar.xz
export PATH=$HOME/ldc2-1.7.0-linux-x86_64/bin:$PATH
export LIBRARY_PATH=$HOME/ldc2-1.7.0-linux-x86_64/lib
git clone --recursive
cd sambamba

To build a development/debug version run

make clean && make debug

To run the test fetch shunit2 from and put it in the path so you can run

make check

See also

GNU Guix

To build sambamba the LDC compiler is also available in GNU Guix:

guix package -i ldc

Compiling for Mac OS X

Sambamba builds on MacOS. We have a Travis integration test as an example. It can be something like

    brew install ldc
    git clone --recursive
    cd sambamba


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

Debugging and troubleshooting

Segfaults on certain Intel Xeons

Important note: some popular Xeon processors segfault under heavy hyper threading - which Sambamba utilizes. Please read this when encountering seemingly random crashes.

Dump core

In a crash sambamba can dump a core file. To make this happen set

ulimit -c unlimited

and run your command. Send us the core file so we can reproduce the state at time of segfault.

Use catchsegv

Another option is to use catchsegv

catchsegv ./build/sambamba command

this will show state on stdout which can be sent to us.

Using gdb

In case of crashes it’s helpful to have GDB stacktraces (bt command). A full stacktrace for all threads:

thread apply all backtrace full

Note that GDB should be made aware of D garbage collector which emits SIGUSR signals and gdb needs to ignore them with

handle SIGUSR1 SIGUSR2 nostop noprint

A binary relocatable install of sambamba with debug information and all dependencies can be fetched from the binary link above. Unpack the tarball and run the contained script with TARGET

./ ~/sambamba-test

Run sambamba in gdb with

gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' \
  --args ~/sambamba-test/sambamba-*/bin/sambamba view --throw-error


Sambamba is generously distributed under GNU Public License v2+.


Citations are the bread and butter of Science. If you are using Sambamba in your research and want to support our future work on Sambamba, please cite the following publication:

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

Bibtex reference

  author = {Tarasov, Artem and Vilella, Albert J. and Cuppen, Edwin and Nijman, Isaac J. and Prins, Pjotr},
  title = {Sambamba: fast processing of NGS alignment formats},
  journal = {Bioinformatics},
  volume = {31},
  number = {12},
  pages = {2032-2034},
  year = {2015},
  doi = {10.1093/bioinformatics/btv098},
  URL = { +}