Sambamba

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, mpileup and depth.

For more information see

 https://github.com/lomereiter/sambamba

The Sambamba paper is published in Bioinformatics (2015) doi: 10.1093/bioinformatics/btv098. Timing logs used in the publication can be found here.