Bismark

Important

Bismark is now the Rust suite, generally available. The bisulfite aligner and methylation tools have been rewritten from Perl to Rust: byte-identical to Perl v0.25.1 on the faithful default path, faster, and lower-memory — and this is the supported default. Get it via Installation (mamba install -c bioconda bismark, cargo, container, or prebuilt binaries) and see the Rust suite overview. The original Perl v0.25.x (the scripts at this repo root) is now legacy / maintenance-freeze (critical fixes only; tagged v0.25.1). New contributions should target the Rust suite — see CONTRIBUTING.md.

See the documentation: https://felixkrueger.github.io/Bismark

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its main features are:

• Bisulfite mapping and methylation calling in one single step
• Supports single-end and paired-end read alignments
• Supports ungapped, gapped or spliced alignments
• Alignment seed length, number of mismatches etc. are adjustable
• Output discriminates between cytosine methylation in CpG, CHG and CHH context

Documentation

The Bismark documentation can be found with the code in the docs subfolder and can also be read online: https://felixkrueger.github.io/Bismark/

There is also an overview of the alignment modes that are currently supported by Bismark: Bismark alignment modes (pdf).

Installation

Bismark is now the Rust suite. Pick one:

# 1. bioconda — also installs the aligners (bowtie2/hisat2/minimap2) for you
mamba install -c bioconda -c conda-forge bismark

# 2. crates.io — installs the whole suite (all tools) into ~/.cargo/bin
cargo install bismark

# 3. Container image (nothing to install; drop-in for nf-core/methylseq)
docker pull ghcr.io/felixkrueger/bismark:latest    # or pin a specific release, e.g. :3.0.0

# 4. Prebuilt binaries — download from the Releases page and put on your PATH
#    https://github.com/FelixKrueger/Bismark/releases

External tools on your PATH: an aligner — Bowtie2 (default), or optionally HISAT2 or minimap2. No Samtools needed — all BAM/SAM/CRAM I/O is pure-Rust. The container bundles the aligners for you. See rust/README.md for details and per-tool installs.

The default bioconda bismark package is now the Rust suite (v3.0.0+); mamba install bismark=0.25.1 still gets the legacy Perl.

Legacy: the Perl Bismark (v0.25.x)

The original Perl scripts remain at this repo root (maintenance-freeze). To use them, download the v0.25.1 release (or mamba install bismark=0.25.1); they need Bowtie2/HISAT2/minimap2 and Samtools on the PATH.

Links

• Bismark Publication: http://www.ncbi.nlm.nih.gov/pubmed/21493656
• Our review about primary data analysis in BS-Seq: http://www.ncbi.nlm.nih.gov/pubmed/22290186

Credits

Bismark was written by Felix Krueger, part of the Babraham Bioinformatics group.

Licences

Bismark itself is free software, bismark report and bismark summary produce HTML graphs powered by Plot.ly which are also free to use and look at!