Fork me on GitHub
Features
  • Powerful filtering with sambamba view --filter
  • Picard-like SAM header merging in the merge tool
  • Optional [==>    ] for operations on whole BAMs
  • Fast copying of a region to a new file with the slice tool
  • Duplicate marking/removal, using the Picard criteria
  • And, of course, the biggest one (yeah, literally!),

    PERFORMANCE    

Benchmarks
Indexing 17GB file on 8 cores, HDD
real time, suser time, s
sambamba3169
samtools7067
Copying reads aligned to the 3rd chr.
to new BAM (8 threads, empty file cache)
real time, suser time, s
sambamba5.838.0
samtools8.533.7
Installation

Precompiled binaries are available for 64-bit systems.

In order to compile from source, install LDC compiler and run in terminal git clone --recursive https://github.com/lomereiter/sambamba.git followed bycd sambamba && make sambamba-ldmd2-64.

License:
GPL v2+
Platforms:
Linux, Mac OS X