Table 4 Features supported by BS-Seeker2, Bismark and BSMAP
From: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
| Â | 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 |