Tool: Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
13
gravatar for William
5.5 years ago by
William4.4k
Europe
William4.4k wrote:

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with BAM files. Current functionality is an important subset of samtools functionality. Because of efficient use of modern multicore CPUs, usually Sambamba is much faster than samtools. For example, indexing an 18 Gb BAM file on a fast 8 core machine utilizes all cores at 45% CPU:

Sambamba index bam:

time ~/sambamba index /scratch/HG00119.mapped.ILLUMINA.bwa.GBR.exome.20111114.bam            
real    1m42.930s
user    6m19.964s
sys     0m32.362s

Samtools index bam:

time ~/samtools index /scratch/HG00119.mapped.ILLUMINA.bwa.GBR.exome.20111114.bam 
real    5m37.669s
user    5m9.127s
sys     0m13.605s

https://github.com/lomereiter/sambamba

bam tool • 4.7k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by William4.4k
1

How many threads were used for the sambamba time?

ADD REPLYlink written 5.5 years ago by Aaronquinlan10k
1

I would also like to know how many concurrent threads were used, but assuming only the userspace code was multithreaded we can do (real - sys) / user which is approximately 5. If the ~45% utilization figure is correct, then 5 * 1.55 = 7.75, so approximately 8 threads.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Matt Shirley8.9k

Completed the quote with the thread info.

ADD REPLYlink written 5.5 years ago by William4.4k

Isn't disk IO the main bottleneck in this operation?

ADD REPLYlink written 5.5 years ago by Christian2.7k

I guess that depends on the storage setup used. The faster the storage you use, the more the speedup is (see results for indexing). https://github.com/lomereiter/sambamba/wiki/Comparison-with-samtools

ADD REPLYlink written 5.5 years ago by William4.4k

How to install and use it correctly? I have:

user@user-MS-7817:~/Documents/sambamba/sambamba$ make sambamba-ldmd2-64
make: *** No rule to make target `sambamba-ldmd2-64'.  Stop.
user@user-MS-7817:~/Documents/sambamba/sambamba$

 

ADD REPLYlink written 3.3 years ago by elvissober20
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