Is sambamba faster than samtools?

Update: January 4, 2022: I didn’t set RAM properly and didn’t have variable BAM depth which is fixed now.

samtools and sambamba are probably the most popular SAM/BAM handling tools. And once you are all set with your analysis setup it all goes down to speed. How do they compare in the most common tasks (view, index, sort, sort -n)? And how does it change with multithreading? Here is my simple summary.

I used human transcriptomic BAM (100k, 1M and 2M aligned reads) and the same for human genomic BAM. Everything ran on Ubuntu 16.04 on SSD (read 560MB/s, write 530MB/s) using time command and getting the real time.

reads	100k	1M	2M
command	samtools | sambamba	samtools | sambamba	samtools | sambamba
index; 1 thread	0m0.148s | 0m0.083s	0m0.983s | 0m0.855s	0m1.902s | 0m1.716s
index; 12 threads	0m0.024s | 0m0.016s	0m0.202s | 0m0.171s	0m0.424s | 0m0.334s
view; 1 thread	0m0.319s | 0m0.099s	0m3.867s | 0m1.126s	0m7.615s | 0m2.235s
view; 12 threads	0m0.075s | 0m0.072s	0m0.663s | 0m0.743s	0m1.355s | 0m1.521s
sort; 1 thread	0m0.812s | 0m0.815s	0m8.434s | 0m8.919s	0m17.051s | 0m17.989s
sort; 12 threads	0m0.132s | 0m0.123s	0m1.522s | 0m1.268s	0m2.918s | 0m2.459s
sort -n; 1 thread	0m1.013s | 0m0.888s	0m11.729s | 0m9.909s	0m23.510s | 0m19.239s
sort -n; 12 threads	0m0.175s | 0m0.135s	0m1.950s | 0m1.328s	0m3.833s | 0m2.766s

Is there a clear winner? I wouldn’t say so. Depends if you have transcriptomic or genomic BAM, how many threads you use, and what command (or their combination) you use.

sambamba seems to be faster in by name sorting (-n) and in genomic sorting in general. samtools is faster in by coordinates transcriptomic sorting. samtools is also faster in multi-threaded view while sambamba is faster in single-thread view. sambamba is slightly faster in indexing of bigger BAMs while indexing of smaller BAMs is 50/50. See Table 3 and Table 4 for recommendations (based on the largest tested BAM).

transcriptome	sort	sort -n	view	index
1 thread	samtools	sambamba	sambamba	sambamba
12 threads	samtools	sambamba	samtools	sambamba

genome	sort	sort -n	view	index
1 thread	sambamba	sambamba	sambamba	sambamba
12 threads	sambamba	sambamba	samtools	sambamba

Note: It is important to realize samtools sort sets RAM per thread while sambamba sort (-m) sets total RAM. By default, samtools uses 768M per thread while sambamba uses 2GB total.

samtools v1.11
sambamba v0.8.0

# sorts
threads=1; input=test.bam; output=foo.bam
samtools sort -@ $threads -m 2G $input > $output
samtools sort -@ $threads -m 2G -n $input > $output
sambamba sort -t $threads -m 2G -o $output $input
sambamba sort -t $threads -m 2G -n -o $output $input

threads=12
samtools sort -@ $threads -m 2G $input > $output
samtools sort -@ $threads -m 2G -n $input > $output
sambamba sort -t $threads -m 24G -o $output $input
sambamba sort -t $threads -m 24G -n -o $output $input 

# index and view
threads=1; output=foo.sam
time samtools index -@ $threads $input > $output
time samtools view -@ $threads -h $input > $output
time sambamba index -t $threads $input > $output
time sambamba view -t $threads -h $input > $output

threads=12
time samtools index -@ $threads $input > $output
time samtools view -@ $threads -h $input > $output
time sambamba index -t $threads $input > $output
time sambamba view -t $threads -h $input > $output