Table 1:

Comparison of leading coverage calculation software tools

		Functionality				Implementation
Tool	Approach	Bases	Blocks	Windows	Language	Intel GKL	Parallelism type	Interface
samtools	Pileup	Yes	No	No	C	No	None	Command line
bedtools	Events	Yes	Yes	No	C++	No	None	Command line
GATK 1	Pileup	Yes	No	No	Java	Yes	Distributed	Command line
sambamba	Pileup	No	Yes	Yes	D	No	Multithreaded	Command line
mosdepth	Events	No	Yes	Yes	Nim	No	Multithreaded2	Command line
SeQuiLa-cov	Events	Yes	Yes	Yes	Scala	Yes	Distributed	Scala, SQL

¹GATK DepthOfCoverage has not yet been ported to the latest version, i.e., GATK 4.x.

²Only for BAM decompression.