A rewrite of the gemBS pipeline framework from Python/C into Rust.
gemBS is a high performance bioinformatic pipeline designed for highthroughput analysis of DNA methylation data from whole genome bisulfites sequencing data (WGBS). It combines GEM3, a high performance read aligner and bs_call, a high performance variant and methyation caller, into a streamlined and efficient pipeline for bisulfite sequence analysis.
The manuscript describing the original gemBS pipeline is available here
The rewrite of the pipeline into Rust has two aims: (1) to have a more robust pipeline and (2) to provide a more flexible platform for future developments. All of the tools developed for the pipeline except for the GEM3 mapper (being an external project that is also very stable!) have now been re-written in Rust. These include bs_call, the methylation and SNV-variant caller, and the methylation and SNP extractions tools mextr and snpxtr. In all cases the running times are comparable to the original C versions.
The pipeline uses samtools for generating sorted BAM/CRAM files from GEM3 and bcftools for merging and indexing BCF files produced by bs_call. In addition, many of the tools link to htslb to enable reading of BAM/CRAM and reading/writing of BCF files. Samtools and htslib are automatically installed during the installation of the gemBS pipeline. There is also an optional dependency on TeXLive which is used to produce pdf versions of the QC reports. If requested by the user this is also installed with the pipeline.
gemBS is licensed under the GPL.
Use git clone --recursive to retrieve the complete source code including the code from external projects such as gem3-mapper.
git clone --recursive https://github.com/heathsc/gemBS-rs.git
Before starting the installation of gemBS, you will need to install or check the installation of several packages.
a) gcc with development libraries
b) rust (for installation instructions see here). Note that if you have rust already installed you should update it using rustup update before trying to compile gemBS.
c) zlib, libz2, lzma, openssl, libcurl, libncurses, wget, expat, ncurses, openssl, freetype, fontconfig
If you are working on a clean (fairly recent) Ubuntu installation, you can install everything required with the following commands:
apt-get install -y build-essential git autoconf wget lbzip2 pkg-config cmake
apt-get install -y zlib1g-dev libbz2-dev libexpat1-dev
apt-get install -y libncurses5-dev liblzma-dev libssl-dev libcurl4-openssl-dev curl
apt-get install -y libfreetype6-dev libfontconfig1-dev
curl https://sh.rustup.rs -sSf > rust.sh && sh rust.sh -y
Download the gemBS distribution if you haven't already done so:
git clone --recursive https://github.com/heathsc/gemBS-rs.git
From the main gemBS-rs directory type the following to make the default config file:
make gemBS_config.mk
Then look at the file gemBS_config.mk and make any changes that are required. When the file is OK the pipeline and components can be built and installed by typing:
make install
If the make and install process is successful, a shell script called gemBS will be created in the main gemBS-rs directory. This file should be copied to a directory that is in your PATH so that gemBS can be invoked from anywhere.
For checking your installation follow this worked example.
Documentation can be found at gemBS.
4.0 First release of gemBS-rs (4th release of gemBS)
4.0.1 Correct bug preventing that caused non-stranded mapping to fail
4.0.2 Move to versions 1.12 of htslib/samtools/bcftools
4.0.2 Change way we iterate over SAM/BAM/CRAM files to the same way used in samtools
view (the old way did not always work with cram files)
4.0.3 Fix problem with reading BCF files from older versions of
gemBS where the CX format string was null terminated
4.0.4 Add max_template_length option to gemBS (option passed on to bs_call)