Bismark pipeline

Bismark specifications

Information


Unique identifier OMICS_00575
Name Bismark
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format SAM, tab-delimited text
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.14.3
Stability Stable
Requirements Bowtie/Bowtie2
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Felix Krueger <>

Publication for Bismark

Bismark IN pipelines

 (21)
2018
PMCID: 5852571
PMID: 29419727
DOI: 10.3390/genes9020075

[…] 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) [18]. cytosine methylation level information was extracted from aligned reads using bismark methylation extractor. a total […]

2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] 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 [32] with maximum 2 mismatches, and only uniquely aligned reads were retained for subsequent analysis. index files were generated using the bismark_genome_preparation […]

2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] genome (grcz10) using the bismark alignment software [32] 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 […]

2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] 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 […]

2018
PMCID: 5905984
PMID: 29668744
DOI: 10.1371/journal.pone.0195972

[…] 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 [15] and the pipeline tool clusterflow [16]. for tsdm libraries the initial 6 base pairs of each reads were ignored in the methylation calling procedure, to avoid random priming […]

Bismark institution(s)
Bioinformatics Group, The Babraham Institute, Cambridge, UK
Bismark funding source(s)
Biotechnology and Biological Sciences Research Council (BBSRC)

Bismark reviews

 (2)
star_border star_border star_border star_border star_border
star star star star star

Miklós Laczik

star_border star_border star_border star_border star_border
star star star star star
Desktop
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!

Shaojun Xie

star_border star_border star_border star_border star_border
star star star star star
Desktop
Bismark is a great tool for the alignment of BS-seq reads.