https://github.com/ccbr/nfcore_methylseq
nf-core Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Science Score: 13.0%
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Low similarity (10.5%) to scientific vocabulary
Last synced: 10 months ago
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nf-core Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Basic Info
- Host: GitHub
- Owner: CCBR
- License: mit
- Language: Nextflow
- Default Branch: master
- Homepage: https://nf-co.re/methylseq
- Size: 19.6 MB
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- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of nf-core/methylseq
Created almost 3 years ago
· Last pushed about 2 years ago
https://github.com/CCBR/nfcore_methylseq/blob/master/
#   [](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+CI%22) [](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/methylseq/results)[](https://doi.org/10.5281/zenodo.1343417) [](https://www.nextflow.io/) [](https://docs.conda.io/en/latest/) [](https://www.docker.com/) [](https://sylabs.io/docs/) [](https://tower.nf/launch?pipeline=https://github.com/nf-core/methylseq) [](https://github.com/askimed/nf-test) [](https://nfcore.slack.com/channels/methylseq)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core) ## Introduction **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results). ## Pipeline Summary The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel). Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. | Step | Bismark workflow | bwa-meth workflow | | -------------------------------------------- | ---------------- | --------------------- | | Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth | | Merge re-sequenced FastQ files | cat | cat | | Raw data QC | FastQC | FastQC | | Adapter sequence trimming | Trim Galore! | Trim Galore! | | Align Reads | Bismark | bwa-meth | | Deduplicate Alignments | Bismark | Picard MarkDuplicates | | Extract methylation calls | Bismark | MethylDackel | | Sample report | Bismark | - | | Summary Report | Bismark | - | | Alignment QC | Qualimap | Qualimap | | Sample complexity | Preseq | Preseq | | Project Report | MultiQC | MultiQC | ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv sample,fastq_1,fastq_2 SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Now, you can run the pipeline using: ```bash nextflow run nf-core/methylseq --input samplesheet.csv --outdir--genome GRCh37 -profile ``` > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters). ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output). ## Credits These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. - Main author: - Phil Ewels ([@ewels](https://github.com/ewels/)) - Maintainers: - Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger)) - Sateesh Peri ([@Sateesh_Peri](https://github.com/sateeshperi)) - Edmund Miller ([@EMiller88](https://github.com/emiller88)) - Contributors: - Rickard Hammarn ([@Hammarn](https://github.com/Hammarn/)) - Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/)) - Patrick Hther ([@phue](https://github.com/phue/)) ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)). ## Citations If you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
Owner
- Name: CCR Collaborative Bioinformatics Resource
- Login: CCBR
- Kind: organization
- Email: nciccbr@mail.nih.gov
- Location: United States of America
- Website: https://bioinformatics.ccr.cancer.gov/ccbr/
- Repositories: 92
- Profile: https://github.com/CCBR
CCR Collaborative Bioinformatics Resource, Center for Cancer Research (NCI), National Institutes of Health