Table 1.

Feature comparison of Bismark and BS Seeker

Feature	Bismark	BS Seeker
Bowtie instances (directional/non-directional)	4	2/4
Single-end (SE)/paired-end (PE) support	Yes/yes	yes/no
Variable read length (SE/PE)	Yes/yes	no/NA
Adjustable insert size (PE)	Yes	NA
Uses basecall qualities for FastQ mapping	Yes	No
Adjustable mapping parameters	5	2
Directional/non-directional library support	Yes/yes	Yes/yesa

^aRequires library to be constructed with an initial sequence tag (Cokus et al., 2008). NA: not available.