Sambamba vs Samtools
Samtools has been the one main tools for reading and writing aligned NGS data since the SAM alignment format was initially proposed. With the amounts of NGS data being generated increasing at a staggering rate, informatic bottlenecks are beginning to appear and there is a rush to make bioinformatics as parallel and scalable as possible. Samtools went parallel only recently, and there is a new competitor to Samtools called Sambamba, so I'll just do a few quick tests to see how it stacks up to Samtools on our 32-core server with 128 GB RAM (standard HDD).
We have an 1.8 GB bam file to work with.
$ du -sh *
1.8G Sequence.bam
Now convert to unsorted sam format. $ samtools view -H Sequence.bam > header.sam
$ samtools view Sequence.bam | shuf \
| cat header.sam - > Sequence_shuf.sam
The sam file is 9.9 GB. Lets try 1-thread SAM-to-BAM conversion and sorting with Samtools.
$ time samtools view -Shb Sequence_shuf.sam \
| samtools sort - Sequence_samtools.test
real 18m52.374s
user 18m30.619s
…
We have an 1.8 GB bam file to work with.
$ du -sh *
1.8G Sequence.bam
Now convert to unsorted sam format. $ samtools view -H Sequence.bam > header.sam
$ samtools view Sequence.bam | shuf \
| cat header.sam - > Sequence_shuf.sam
The sam file is 9.9 GB. Lets try 1-thread SAM-to-BAM conversion and sorting with Samtools.
$ time samtools view -Shb Sequence_shuf.sam \
| samtools sort - Sequence_samtools.test
real 18m52.374s
user 18m30.619s
…