![]() If it is software development related, I have posted a new issue on the issue tracker or added to an existing one. ![]() If it is a support/install question, I have posted it to the mailing list.I have read and agreed to the below code of conduct.I have tried the latest release of Sambamba.I have searched for it on the mailing list.I have searched for it on the issue tracker (also check closed issues).When reporting an issue, include the output of the program and the contents of the output directory. The issue tracker is for development issues around the software itself. Support/installation questions should be aimed at the mailing list. Also try running the latest version of Sambamba to make sure it has not been fixed already. It is likely someone may have encountered something similar. Reporting a Ssambamba Bug or Issueīefore posting an issue, search the issue tracker and mailing list first. Users of Homebrew can also use the formula from homebrew-bio.įor installation help and general discussion. The development version is packaged here. GNU Guix InstallĪ reproducible GNU Guix package for Sambamba is available. There should be binary downloads for Linux and MacOS. Provide recent binary installs for Linux. The tarball, unpack it, and run it according to the accompanyingīelow package managers Conda, GNU Guix, Debian and Homebrew also To use CRAM, you can still use one of the older (binary)īinary Installation Install Stable Releaseįor those not in the mood to learn/install new package managers, there Important Notice: With version 0.8 support for CRAM was removed from To know more about what is available and how to use it.įor more information on Sambamba, contact the mailing list (see Getting help). Sambamba is free and open source software, licensed under GPLv2+. 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. The D language is extremely suitable for high performance computing (HPC). slice quickly extracts a region into a new file, tweaking only first/last chunks.markdup, a fast implementation of Picard algorithm.Chanjo builds upon this and gets you to exon/gene levels of abstraction.depth allows to measure base, sliding window, or region coverages.view -L utilizes BAM index to skip unrelated chunks.Automatic index creation when writing any coordinate-sorted file.Fast large machine sort, see performance.In addition, Sambamba has a few interesting features to offer. For sort, Sambamba has been beaten, though Sambamba is notably up to 2x faster than samtools on large RAM machines (120GB+). For markdup, almost 6x faster, and for view, 4x faster. For example, for flagstat, Sambamba is 1.4x faster than samtools. A recent performance comparison shows that Sambamba still holds its ground and can even do better. In March 2017, samtools 1.4 was released, reaching some parity. When we started writing Sambamba in 2012, the mainĪdvantage over samtools was parallelized BAM reading and writing. Just specify /dev/stdin or /dev/stdout asįilenames. To cite Sambamba, see Credit.Ĭurrent functionality is an important subset of samtoolsįunctionality including view, index, sort, markdup, and depth. As of January 2023, Sambamba has been cited over 1000 times and has been installed from Conda over 250,000 times. Because of its efficiency, Sambamba is an important work horse running in many sequencing centers around the world today. 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. ![]() ![]() After 10 years and over one thousand citations we can announce sambamba 1.0 stable! January 2023: announcing v1.0 release of the great sambamba tool!Ī minor fix and a major release. ![]() Sambamba: fast processing of NGS alignment formats. ![]()
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