https://github.com/lieberinstitute/biocmap
Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
https://github.com/lieberinstitute/biocmap
nextflow wgbs
Last synced: over 1 year ago
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Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
- Host: GitHub
- URL: https://github.com/lieberinstitute/biocmap
- Owner: LieberInstitute
- Created: 2019-11-22T16:36:22.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-09-15T16:55:27.000Z (almost 3 years ago)
- Last Synced: 2025-01-28T16:45:50.945Z (over 1 year ago)
- Topics: nextflow, wgbs
- Language: HTML
- Homepage: http://research.libd.org/BiocMAP/
- Size: 177 MB
- Stars: 3
- Watchers: 5
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://zenodo.org/badge/latestdoi/223444482)
# BiocMAP
BiocMAP is a **Bioc**onductor-friendly **M**ethylation **A**nalysis **P**ipeline. It consists of two [nextflow](https://www.nextflow.io/)-based "modules", which together take a set of FASTQ files, described in [a `samples.manifest` file](http://research.libd.org/BiocMAP/inputs.html#the-samples.manifest-file), and ultimately produce [bsseq](https://www.bioconductor.org/packages/release/bioc/vignettes/bsseq/inst/doc/bsseq.html) R objects containing methylation data and an R data frame of alignment and quality metrics.
The first BiocMAP module performs speedy alignment to a reference genome by [Arioc](https://github.com/RWilton/Arioc), and requires GPU resources. Methylation extraction and remaining steps are performed in the second module, optionally on a different computing system where GPUs need not be available.
## Features
- GPU-accelerated alignment to a reference genome via [Arioc](https://github.com/RWilton/Arioc)
- Memory-efficient, HDF5-backed [bsseq](https://www.bioconductor.org/packages/release/bioc/vignettes/bsseq/inst/doc/bsseq.html) output objects immediately ready for analysis with [Bioconductor](https://bioconductor.org/)/R packages of choice
- Automatic management of [reference files](http://research.libd.org/BiocMAP/annotation.html), allowing simple configuration of [GENCODE](https://www.gencodegenes.org/) release and [other settings](http://research.libd.org/BiocMAP/annotation.html#choosing-build), while alternatively [supporting user-provided files](http://research.libd.org/BiocMAP/annotation.html#custom-annotation)
- [Support for docker and singularity](http://research.libd.org/BiocMAP/setup-details.html#installation) for flexible and reproducible installation
- Automatically merge samples split across multiple FASTQ files, using [the `samples.manifest` input](http://research.libd.org/BiocMAP/inputs.html#the-samples.manifest-file)
## Get started
[The BiocMAP documentation website](http://research.libd.org/BiocMAP/index.html) provides a complete description of features, installation, and many other details. To quickly get started, see our [quick-start guide](http://research.libd.org/BiocMAP/quick-start.html).
We provide [shell scripts](http://research.libd.org/BiocMAP/quick-start.html#your-main-script) for out-of-the-box execution a [SLURM](https://slurm.schedmd.com/overview.html) or [SGE](https://docs.oracle.com/cd/E19279-01/820-3257-12/n1ge.html)-based computing cluster, or for execution on a Linux-based machine. Software dependencies can be installed via the shell script `install_software.sh`, which makes use of docker or Anaconda/Miniconda.
## Authors
[Nick Eagles](https://github.com/Nick-Eagles)
## Cite
We hope `BiocMAP` will be a useful tool for your research. Please use the following bibtex information to cite this software. Thank you!
```
@article {Eagles2022.04.20.488947,
author = {Eagles, Nicholas J and Wilton, Richard and Jaffe, Andrew E. and Collado-Torres, Leonardo},
title = {BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data},
year = {2022},
doi = {10.1101/2022.04.20.488947},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://doi.org/10.1101/2022.04.20.488947},
journal = {bioRxiv}
}
```
## Contact
[Leonardo Collado-Torres](http://lcolladotor.github.io/)