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Table 4 Features supported by BS-Seeker2, Bismark and BSMAP

From: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

  BS-Seeker2 Bismark BSMAP
Support local alignment Yes No No
Tailored for one restriction enzyme RRBS Yes No Yes
Map to reduced representation genome for RRBS Yes No No
Option for removing un-converted reads Yes No No
Tailored for double-restriction enzyme RRBS Yes No No
# of supported input formats 4 2 3
# of supported output formats 3 1 3
Build-in adapter removing function Yes No Yes
Generate wiggle file for methylation levels Yes No No
Report reads coverage for AT Yes No No
Able to manipulate all the parameters of Bowtie(2) Yes No -
Programming language Python Perl C++
Mapping strategy 3-letter 3-letter wild-card
Available in Galaxy Toolshed Yes Yes Yes
Gapped alignment Yes Yes Yes
Call methylation for CG Yes Yes Yes
Support directional/non-directional sequencing Yes/Yes Yes/Yes Yes/Yes
Support Single-end/Paired-end sequencing Yes/Yes Yes/Yes Yes/Yes