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reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bam","bioinformatics","sam"],"created_at":"2024-08-03T01:00:52.602Z","updated_at":"2026-02-18T20:32:40.198Z","avatar_url":"https://github.com/biod.png","language":"D","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/biod/sambamba.svg?branch=master)](https://travis-ci.org/biod/sambamba) [![DL](https://anaconda.org/bioconda/sambamba/badges/downloads.svg)](https://anaconda.org/bioconda/sambamba) [![BrewBadge](https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg)](https://github.com/brewsci/homebrew-bio) [![GuixBadge](https://img.shields.io/badge/gnuguix-sambamba-brightgreen.svg)](https://packages.guix.gnu.org/packages/sambamba/) [![DebianBadge](https://badges.debian.net/badges/debian/testing/sambamba/version.svg)](https://packages.debian.org/testing/sambamba)\n\nA. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. [Sambamba: fast processing of NGS alignment formats](https://doi.org/10.1093/bioinformatics/btv098). Bioinformatics, 2015.\n\n# SAMBAMBA\n\nTable of Contents\n=================\n\n   * [Introduction](#introduction)\n   * [Binary Installation](#binary-installation)\n      * [Install Stable Release](#install-stable-release)\n      * [Bioconda Install](#bioconda-install)\n      * [GNU Guix Install](#gnu-guix-install)\n      * [Debian GNU/Linux Install](#debian-gnulinux-install)\n      * [Homebrew Install](#homebrew-install)\n   * [Getting Help](#getting-help)\n      * [Reporting a Sambamba Bug or Issue](#reporting-a-sambamba-bug-or-issue)\n      * [Checklist](#checklist)\n      * [Code of Conduct](#code-of-conduct)\n   * [Compiling Sambamba](#compiling-sambamba)\n      * [Compilation Dependencies](#compilation-dependencies)\n      * [Compiling for Linux](#compiling-for-linux)\n         * [GNU Guix](#gnu-guix)\n      * [Compiling for Mac OS X](#compiling-for-mac-os-x)\n      * [Development](#development)\n   * [Debugging and Troubleshooting](#debugging-and-troubleshooting)\n      * [Segfaults on Certain Intel Xeons](#segfaults-on-certain-intel-xeons)\n      * [Dump Core](#dump-core)\n      * [Use catchsegv](#use-catchsegv)\n\n* [Using GDB](#using-gdb)\n   * [License](#license)\n   * [Credit](#credit)\n\n\n\u003ca name=\"intro\"\u003e\u003c/a\u003e\n# Introduction\n\n*January 2023*: announcing v1.0 release of the great sambamba tool!\n\nA minor fix and a major release. After 10 years and over one thousand citations we can announce sambamba 1.0 stable!\n\nSambamba 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 centers around the world today. As of January 2023, Sambamba has been cited over [1000 times](http://scholar.google.nl/citations?hl=en\u0026user=5ijHQRIAAAAJ) and has been installed from Conda over [250,000 times](https://anaconda.org/bioconda/sambamba). Sambamba is also distributed by [Debian](https://packages.debian.org/testing/sambamba). To cite Sambamba, see [Credit](#credit).\n\nCurrent functionality is an important subset of `samtools`\nfunctionality including view, index, sort, markdup, and depth. Most\ntools support piping. Just specify `/dev/stdin` or `/dev/stdout` as\nfilenames. When we started writing Sambamba in 2012, the main\nadvantage over `samtools` was parallelized BAM reading and writing.\n\nIn March 2017, `samtools` 1.4 was released, reaching some parity. A [recent performance comparison](https://github.com/guigolab/sambamBench-nf) shows that Sambamba still holds its ground and can even do better. Here are some comparison [metrics](https://public-docs.crg.es/rguigo/Data/epalumbo/sambamba_ws_report.html). 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+).\n\nIn addition, Sambamba has a few interesting features to offer. In particular:\n\n* Fast large machine `sort`, see [performance](./test/benchmark/stats.org)\n* Automatic index creation when writing any coordinate-sorted file\n* `view -L \u003cbed file\u003e` utilizes BAM index to skip unrelated chunks\n* `depth` allows to measure base, sliding window, or region coverages\n  * [Chanjo](https://www.chanjo.co/) builds upon this and gets you to exon/gene levels of abstraction\n* `markdup`, a fast implementation of Picard algorithm\n* `slice` quickly extracts a region into a new file, tweaking only first/last chunks\n* ...and more (you'll have to try)\n\nThe 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 reference guided sequencing data, and we aim to make it easy to parse and process BAM files.\n\nSambamba is free and open source software, licensed under GPLv2+.\nSee manual pages [online](https://lomereiter.github.io/sambamba/docs/sambamba-view.html)\nto know more about what is available and how to use it.\n\nFor more information on Sambamba, contact the mailing list (see [Getting help](#getting-help)).\n\n## No CRAM Support\n\n**Important Notice: With version 0.8 support for CRAM was removed from\nSambamba (see the [RELEASE NOTES](./RELEASE-NOTES.md))**\n\nTo use CRAM, you can still use one of the older (binary)\n[releases](https://github.com/biod/sambamba/releases) of Sambamba.\n\n\u003ca name=\"install\"\u003e\u003c/a\u003e\n# Binary Installation\n## Install Stable Release\n\nFor those not in the mood to learn/install new package managers, there\nare Github source and binary\n[releases](https://github.com/biod/sambamba/releases). Simply download\nthe tarball, unpack it, and run it according to the accompanying\nrelease notes.\n\nBelow package managers Conda, GNU Guix, Debian and Homebrew also\nprovide recent binary installs for Linux.  For MacOS you may use Conda\nor Homebrew.\n\n## Bioconda Install\n\n[![Install with CONDA](https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg)](https://anaconda.org/bioconda/sambamba)\n\nThere should be binary downloads for Linux and MacOS.\n\nWith Conda use the [`bioconda`](https://bioconda.github.io/) channel.\n\n## GNU Guix Install\n\n[![GuixBadge](https://img.shields.io/badge/gnuguix-sambamba--0.6.8-brightgreen.svg)](https://www.gnu.org/software/guix/packages/S/)\n\nA reproducible [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for Sambamba is available. The development version is packaged [here](https://gitlab.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/sambamba.scm).\n\n## Debian GNU/Linux Install\n\n[![DebianBadge](https://badges.debian.net/badges/debian/testing/sambamba/version.svg)](https://packages.debian.org/testing/sambamba)\n\nSee also Debian package [status](https://tracker.debian.org/pkg/sambamba).\n\n## Homebrew Install\n\n[![BrewBadge](https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg)](https://github.com/brewsci/homebrew-bio)\n\nUsers of Homebrew can also use the formula from [homebrew-bio](https://github.com/brewsci/homebrew-bio).\n\n    brew install brewsci/bio/sambamba\n\nIt should work for Linux and MacOS.\n\n\u003ca name=\"help\"\u003e\u003c/a\u003e\n# Getting Help\n\nSambamba has a\n[mailing list](https://groups.google.com/forum/#!forum/sambamba-discussion)\nfor installation help and general discussion.\n\n## Reporting a Ssambamba Bug or Issue\n\nBefore posting an issue, search the issue tracker and [mailing list](https://groups.google.com/forum/#!forum/sambamba-discussion) 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.\n\nPlease use the following checklist. It exists for multiple reasons. :)\n\n## Checklist\n\n1. [X] I have found an issue with Sambamba\n2. [ ] I have searched for it on the [issue tracker](https://github.com/biod/sambamba/issues) (also check closed issues)\n3. [ ] I have searched for it on the [mailing list](https://groups.google.com/forum/#!forum/sambamba-discussion)\n4. [ ] I have tried the latest [release](https://github.com/biod/sambamba/releases) of Sambamba\n5. [ ] I have read and agreed to the below code of conduct\n6. [ ] If it is a support/install question, I have posted it to the [mailing list](https://groups.google.com/forum/#!forum/sambamba-discussion)\n7. [ ] If it is software development related, I have posted a new issue on the [issue tracker](https://github.com/biod/sambamba/issues) or added to an existing one\n8. [ ] In the message, I have included the output of my Sambamba run\n9. [ ] In the message, I have included relevant files in the output directory\n10. [ ] (Optional) I have made the data available to reproduce the problem\n\nTo 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.\n\n## Code of Conduct\n\nBy using Sambamba and communicating with its community, you implicitly agree to abide by the [code of conduct](https://software-carpentry.org/conduct/) as published by the Software Carpentry initiative.\n\n\n\u003ca name=\"compile\"\u003e\u003c/a\u003e\n# Compiling Sambamba\n\nNote: In general, there is no need to compile Sambamba. You can use a recent binary install as listed above.\n\nThe preferred method for compiling Sambamba is with the LDC compiler which targets LLVM. LLVM version 6 is faster than earlier editions.\n\n## Compilation Dependencies\n\nSee [INSTALL.md](./INSTALL.md).\n\n## Compiling for Linux\n\nThe LDC compiler's Github repository provides binary images. The current preferred release for Sambamba is LDC - the LLVM D compiler (\u003e= 1.6.1). After installing LDC from https://github.com/ldc-developers/ldc/releases/ with, for example\n\n```sh\ncd\nwget https://github.com/ldc-developers/ldc/releases/download/v$ver/ldc2-1.7.0-linux-x86_64.tar.xz\ntar xvJf ldc2-1.7.0-linux-x86_64.tar.xz\nexport PATH=$HOME/ldc2-1.7.0-linux-x86_64/bin:$PATH\nexport LIBRARY_PATH=$HOME/ldc2-1.7.0-linux-x86_64/lib\n```\n\n```sh\ngit clone --recursive https://github.com/biod/sambamba.git\ncd sambamba\nmake\n```\n\nTo build a development/debug version run\n\n```sh\nmake clean \u0026\u0026 make debug\n```\n\nTo run the test, fetch shunit2 from https://github.com/kward/shunit2 and put it in the path so\nyou can run\n\n```sh\nmake check\n```\n\nSee also [INSTALL.md](./INSTALL.md).\n\n### GNU Guix\n\nOur development and release environment is GNU Guix.  To build\nsambamba the LDC compiler is also available in GNU Guix:\n\n```sh\nguix package -A ldc\n```\n\nFor more instructions see [INSTALL.md](./INSTALL.md).\n\n## Compiling with Meson/Ninja\n\nDebian uses a Meson+Ninja build. It may work with something like\n\n```sh\nmeson build\ncd build\nninja\nninja test\n\ntime ./build/sambamba sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam\nsambamba 1.0.1\n by Artem Tarasov and Pjotr Prins (C) 2012-2023\n    LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)\nreal    0m13.343s\nuser    2m11.663s\nsys     0m4.232s\n```\n\nor possibly with some additional tuning runtimes get close to the optimized static build (see [benchmarks](test/benchmark/stats.org).\n\n```sh\nrm -rf build/ ; env D_LD=gold CC=gcc meson build --buildtype release\ncd build/\nenv CC=gcc ninja\nenv CC=gcc ninja test\n\ntime ./build/sambamba sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam\nsambamba 1.0.1\n by Artem Tarasov and Pjotr Prins (C) 2012-2023\n    LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)\nreal    0m10.227s\nuser    2m7.203s\nsys     0m4.039s\n```\n\n## Compiling for MacOS\n\nSambamba builds on MacOS. We have a Travis [integration test](https://travis-ci.org/pjotrp/sambamba) as\nan example. It can be something like\n\n```sh\n    brew install ldc\n    git clone --recursive https://github.com/biod/sambamba.git\n    cd sambamba\n    make\n```\n\n## Development\n\nSambamba development and issue tracker is on\n[github](https://github.com/biod/sambamba). Developer\ndocumentation can be found in the source code and the [development\ndocumentation](https://github.com/biod/sambamba-dev-docs).\n\n\u003ca name=\"debug\"\u003e\u003c/a\u003e\n\n# Debugging and Troubleshooting\n\n## Segfaults on Certain Intel Xeons\n\nImportant Note: Some older Xeon processors segfault under heavy hyper\nthreading - which Sambamba utilizes.  Please read\n[this](https://blog.cloudflare.com/however-improbable-the-story-of-a-processor-bug/)\nwhen encountering seemingly random crashes. There is no real fix other\nthan disabling hyperthreading. Also discussed [here](https://github.com/biod/sambamba/issues/335). Thank Intel for producing this bug.\n\n## Dump Core\n\nIn a crash, Sambamba can dump a core file. To make this happen set\n\n```sh\nulimit -c unlimited\n```\n\nand run your command. Send us the core file so we can reproduce the state at\ntime of segfault.\n\n## Use catchsegv\n\nAnother option is to use `catchsegv`\n\n```sh\ncatchsegv ./build/sambamba command\n```\n\nThis will show state on stdout which can be sent to us.\n\n## Using GDB\n\nIn case of crashes, it's helpful to have GDB stacktraces (`bt`\ncommand). A full stacktrace for all threads:\n\n```\nthread apply all backtrace full\n```\n\nNote that GDB should be made aware of D garbage collector, which emits\nSIGUSR signals and GDB needs to ignore them with\n\n```\nhandle SIGUSR1 SIGUSR2 nostop noprint\n```\n\nA binary, relocatable install of Sambamba with debug information and\nall dependencies can be fetched from the binary link above.  Unpack\nthe tarball and run the contained install.sh script with TARGET\n\n```\n./install.sh ~/sambamba-test\n```\n\nRun Sambamba in GDB with\n\n```\ngdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' \\\n  --args ~/sambamba-test/sambamba-*/bin/sambamba view --throw-error\n```\n\n\u003ca name=\"license\"\u003e\u003c/a\u003e\n# License\n\nSambamba is generously distributed under GNU Public License v2+.\n\n\u003ca name=\"credits\"\u003e\u003c/a\u003e\n# Credit\n\nCitations 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:\nA. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. [Sambamba: fast processing of NGS alignment formats](https://doi.org/10.1093/bioinformatics/btv098). Bioinformatics, 2015.\n\n## Bibtex reference\n\n```bibtex\n\n@article{doi:10.1093/bioinformatics/btv098,\n  author = {Tarasov, Artem and Vilella, Albert J. and Cuppen, Edwin and Nijman, Isaac J. and Prins, Pjotr},\n  title = {Sambamba: fast processing of NGS alignment formats},\n  journal = {Bioinformatics},\n  volume = {31},\n  number = {12},\n  pages = {2032-2034},\n  year = {2015},\n  doi = {10.1093/bioinformatics/btv098},\n  URL = { + http://dx.doi.org/10.1093/bioinformatics/btv098}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiod%2Fsambamba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiod%2Fsambamba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiod%2Fsambamba/lists"}