Bismark statistics

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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

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Publication for Bismark

Bismark in pipelines

 (57)
2018
PMCID: 5828664
PMID: 29412141
DOI: 10.7554/eLife.31977.047

[…] spike-in of 5%) to obtain high-coverage read data. the obtained reads were trimmed using a customized python3 script (10 bp at the start and 15 bp at the end) and aligned to hg19 using the software bismark (settings: l,0,–0.6, version 0.12.5, rrid:scr_005604)(). specifically, paired-end alignment of trimmed reads was performed and unmapped reads from read one were realigned using bismark […]

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

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 [] 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 biases. […]

2018
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] reads on a hiseq 2500 by the genome technology center at new york university (nyu)., rrbs fastq files were quality trimmed using fastqc (v0.11.5) and mapped to the mouse genome (mm9) using bismark (v0.16.3) using the following options: “--bam --chunkmbs 1024 –multicore 8”. mapped bam files were sorted with samtools (v0.1.19-96b5f2294a) and methylation calls were extracted using […]


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Bismark in publications

 (232)
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] reads on a hiseq 2500 by the genome technology center at new york university (nyu)., rrbs fastq files were quality trimmed using fastqc (v0.11.5) and mapped to the mouse genome (mm9) using bismark (v0.16.3) using the following options: “--bam --chunkmbs 1024 –multicore 8”. mapped bam files were sorted with samtools (v0.1.19-96b5f2294a) and methylation calls were extracted using […]

PMCID: 5904126
PMID: 29666375
DOI: 10.1038/s41398-018-0130-x

[…] identified using the illumina hiseq x ten platform with an average of about 700 million (±75 million) 150-bp paired-end reads per sample. clean reads were mapped to the hg19 reference genome using bismark. we first combined two strands of information of cpg sites and then excluded those cpgs with <5 reads or that overlapped with common variants in the chinese han genome (maf > 0.05). […]

PMCID: 5907189
PMID: 29669513
DOI: 10.1186/s12864-018-4666-1

[…] version. the human reference genome sequence hg19 in the ucsc database was used for comparison or analysis with the ensembl 75 annotation database. for mapping of bisulfite-converted reads, we used bismark [], which provides the minimized bias result by using a best-hit alignment strategy. in order to improve the accuracy of bisulfite alignment, we designated -n parameter as 0 (maximal […]

PMCID: 5899405
PMID: 29653520
DOI: 10.1186/s12864-018-4640-y

[…] allele, with a minimum coverage of 5, an average mapping quality above 15 and a maf of greater than 0.1 []., the sequencing datasets for the samples were mapped to the extended probe sequence using bismark, an aligner and methylation caller designed specifically for bisulphite treated sequence data. sequencing reads were mapped as fragment reads rather than paired-end; a mismatch number of 3 […]

PMCID: 5899322
PMID: 29653584
DOI: 10.1186/s13073-018-0534-5

[…] with 150-bp, paired-end reads. raw reads were trimmed for adapter and transposon sequences and only bases with a quality value below 30 were kept using cutadapt 1.10. reads were then mapped by bismark 0.15.0 [] with bowtie 2.2.5 [] to the mouse reference genome (mm10). methylation ratios were extracted using bismark and analyzed using r with the package bsseq []., to investigate potential […]


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

Bismark reviews

 (2)
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Miklós Laczik

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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

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