- Unique identifier:
- Command line interface
- Input format:
- Operating system:
- GNU General Public License version 2.0
- Software type:
- Restrictions to use:
- Output format:
- SAM, tab-delimited text
- Programming languages:
- Computer skills:
- Felix Krueger <>
No open topic.
(Krueger and Andrews, 2011)
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
PMID: 21493656 DOI: 10.1093/bioinformatics/btr167
Bioinformatics Group, The Babraham Institute, Cambridge, UK
Biotechnology and Biological Sciences Research Council (BBSRC)
2 user reviews
2 user reviews
Bismark is the definitive tool for (primary and secondary) bisulfite sequencing analysis. It is easy to use, very stable, well maintained, I had zero issues with it over the years. Not only it aligns the reads to a reference genome, it's methylation extractor module produces various useful outputs in standard formats (sam, bam, bedGraph etc.) which are customizable too (e.g. separate results by strand, show only CpGs or CHG, CHH contexts separately, show data on all Cs on a genome or only the covered ones, produce UCSC compatible bedGraph files with 0-based half-open coordinates or alternative tab delimited files with 1-based coordinates, it can remove spaces from read names etc.); it really opens the door for all types of downstream analyses. The documentation is also superb, very well written with clear examples and a complete guide with all options, it leaves nothing to guess. There are even specific analysis recommendations for different applications and commercially available kits (e.g. when to remove duplicates, when to expect a non-directional library etc.). I'm generally a big fan of Babraham tools, Iáve been using Bismark for at least 5 years for RRBS and WGBS, it's still my number one choice and it gets better and better.
If I really want to nitpick and find a negative point, I would say the parallelization is a bit of a hassle if you have limited resources, it's not as straightforward as setting the number of threads to use, you need some experimenting with parameters like --multicore and -p to find out how many actual cores (and RAM) are used for a typical run with your settings. Also, itás not the fastest tool in the world, for example BSMAP is said to be faster (especially in RRBS mode), but then again in side-by-side comparisons I always managed to map more reads with Bismark, and I think the speed is quite reasonable, I'm happy with it.
Overall Bismark is a wonderful tool, I can highly recommend it for any (RR)BS data analysis!