The Burrows Wheeler Aligner with networking capabilities. The unmaintainable multi-threading code was removed from upstream BWA and a new function 'bwa bam2bam' was added.

This function adds a new workflow that reads a BAM file and writes a BAM file, in a single invocation and with no intermediate files. It uses 0MQ (ZeroMQ) to allow multithreading and network transparent multiprocessing.

Why would anyone want this? First off, the simple workflow makes life easy. Second, if you're aligning lots of data and running on a single machine becomes impractical, you will be happy about this program, which distributes work on the fly to a fully dynamic network of cooperating processes and machines.

To use the improved workflow, run something like

bwa bam2bam input.bam -f output.bam -t 8

This would run locally with 8 worker threads, handling everything (both single ended and paired end reads) automatically. To make use of the network distribution, run

bwa bam2bam input.bam -f output.bam -t 0 -p PORT

where PORT is a free port number. Then run many instances of this

bwa worker -h HOST -p PORT -t N

where HOST and PORT denote the host running 'bam2bam' and N is the number of desired worker threads. Bwa doesn't case how these jobs are started, so you can use any load balancer or grid scheduler you happen to run.