Sambamba: process your BAM data faster!

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, s	user time, s
sambamba	31	69
samtools	70	67

Copying reads aligned to the 3rd chr.
to new BAM (8 threads, empty file cache)

	real time, s	user time, s
sambamba	5.8	38.0
samtools	8.5	33.7

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