Forum:Faster Bam Sorting With Samtools And Rocksdb

Question

[Chris Miller]

Faster BAM Sorting with SAMtools and RocksDB

http://devblog.dnanexus.com/faster-bam-sorting-with-samtools-and-rocksdb/

We’ve been hacking on a fork of samtools providing a new command, samtools rocksort, capable of sorting large BAMs significantly faster than samtools sort on modern server hardware. It leverages the flexible external sorting and compaction algorithms in RocksDB, Facebook’s recently open-sourced embedded storage engine (itself a descendant of Google’s LevelDB).

Cool stuff.