|Interface||Command line interface|
|Restrictions to use||None|
|Output format||SAM, tab-delimited text|
|License||GNU General Public License version 2.0|
Add your version
- person_outline Felix Krueger <>
Publication for Bismark
Bismark IN pipelines(21)
[…] score q < 30) were excluded. after all quality checks, bisulfite short sequences were aligned to the a. thaliana from arabidopsis information resource version 10 (tair 10) reference genome using bismark aligner (v 0.14.5) with default parameters (n = 1 and l = 50) . cytosine methylation level information was extracted from aligned reads using bismark methylation extractor. a total […]
[…] reads from errbs libraries were identified using standard illumina base-calling software., raw reads were pre-processed using trimgalore and aligned to the zebrafish genome (grcz10) using the bismark alignment software  with maximum 2 mismatches, and only uniquely aligned reads were retained for subsequent analysis. index files were generated using the bismark_genome_preparation […]
[…] genome (grcz10) using the bismark alignment software  with maximum 2 mismatches, and only uniquely aligned reads were retained for subsequent analysis. index files were generated using the bismark_genome_preparation command and the entire reference genome. the –non_directional parameter was applied while running bismark. all other parameters were set to default. filled-in nucleotides […]
[…] retained for subsequent analysis. index files were generated using the bismark_genome_preparation command and the entire reference genome. the –non_directional parameter was applied while running bismark. all other parameters were set to default. filled-in nucleotides were trimmed off when doing methylation calling. the methylation level of each sampled cytosine was estimated as the number […]
[…] of r1 to remove bases derived from the sequence tag introduced in the library preparation procedure. alignment to the human reference assembly grch37 and methylation calling was performed with the bismark software  and the pipeline tool clusterflow . for tsdm libraries the initial 6 base pairs of each reads were ignored in the methylation calling procedure, to avoid random priming […]
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!