Bismark determines uniquely best alignments, it is less likely to report non-unique alignments; however, this comes at the cost of a slightly increased run time (for details see Supplementary Material). Table 1.Feature comparison of Bismark and BS SeekerFeatureBismarkBS SeekerBowtie instances (directional/non-directional)42/4Single-end (SE)/paired-end (PE) supportYes/yesyes/noVariable read length (SE/PE)Yes/yesno/NAAdjustable insert size (PE)YesNAUses basecall qualities for FastQ mappingYesNoAdjustable mapping parameters52Directional/non-directional library supportYes/yesYes/yesaaRequires library to be constructed with an initial sequence tag (Cokus et al., 2008). NA: not available.
