{"id":48573044,"url":"https://github.com/vibtobilab/methylseq","last_synced_at":"2026-05-19T12:01:21.404Z","repository":{"id":304853003,"uuid":"1020259468","full_name":"VIBTOBIlab/MethylSeq","owner":"VIBTOBIlab","description":"Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel","archived":false,"fork":false,"pushed_at":"2026-05-19T10:18:55.000Z","size":20823,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-19T11:35:32.327Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/VIBTOBIlab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-07-15T15:30:34.000Z","updated_at":"2026-05-19T09:53:57.000Z","dependencies_parsed_at":"2025-07-16T15:39:10.955Z","dependency_job_id":"b269508b-e68b-47b4-a8a8-7c711686439c","html_url":"https://github.com/VIBTOBIlab/MethylSeq","commit_stats":null,"previous_names":["vibtobilab/methylseq"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/VIBTOBIlab/MethylSeq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIBTOBIlab%2FMethylSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIBTOBIlab%2FMethylSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIBTOBIlab%2FMethylSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIBTOBIlab%2FMethylSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VIBTOBIlab","download_url":"https://codeload.github.com/VIBTOBIlab/MethylSeq/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIBTOBIlab%2FMethylSeq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33215440,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-19T07:54:09.561Z","status":"ssl_error","status_checked_at":"2026-05-19T07:54:08.508Z","response_time":58,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-04-08T15:30:43.491Z","updated_at":"2026-05-19T12:01:21.384Z","avatar_url":"https://github.com/VIBTOBIlab.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MethylSeq pipeline of TOBI lab\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.4-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)\n\n## Introduction\n\n\u003e **Note:** This pipeline has been modified using the original nf-core/methylseq pipeline (version 2.6.0) to include the optical removal duplicates and some other modules in the Bismark subworkflow. You can find the original pipeline at the following [nfcore repository](https://nf-co.re/methylseq/2.6.0).\n\n**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.\n\nThe 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.\n\nOn 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).\n\n## Pipeline Summary\n\nThe 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).\nChoose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`.\n\n| Step                                         | Bismark workflow      | bwa-meth workflow     |\n| -------------------------------------------- | --------------------- | --------------------- |\n| Generate Reference Genome Index _(optional)_ | Bismark               | bwa-meth              |\n| Merge re-sequenced FastQ files               | cat                   | cat                   |\n| Raw data QC                                  | FastQC                | FastQC                |\n| Adapter sequence trimming                    | Trim Galore!          | Trim Galore!          |\n| Align Reads                                  | Bismark               | bwa-meth              |\n| Filter Non Conversion                        | Bismark               | -                     |\n| Deduplicate Alignments                       | Bismark               | Picard MarkDuplicates |\n| Removal of optical duplicates                | Picard MarkDuplicates | -                     |\n| Extract methylation calls                    | Bismark               | MethylDackel          |\n| Sample report                                | Bismark               | -                     |\n| Summary Report                               | Bismark               | -                     |\n| Alignment QC                                 | Qualimap              | Qualimap              |\n| Sample complexity _(optional)_               | Preseq                | Preseq                |\n| CpGs-level saturation _(optional)_           | methurator            | methurator            |\n| Project Report                               | MultiQC               | MultiQC               |\n\n## Usage\n\n\u003e [!NOTE]\n\u003e 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.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nSRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz\nSRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz\nSRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz\nEcoli_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\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run main.nf --input samplesheet.csv --outdir \u003cOUTDIR\u003e --genome GRCh37 -profile \u003cdocker/singularity/podman/shifter/charliecloud/conda/institute\u003e\n```\n\n\u003e [!WARNING]\n\u003e 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**_;\n\u003e see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/2.6.0/docs/usage), the [parameter documentation](https://nf-co.re/methylseq/2.6.0/parameters) and the section below for the parameters that have been added to the modifed version of the pipeline.\n\n## Parameters included in the modified version\n\nThe original [nf-core/methylseq pipeline](https://nf-co.re/methylseq/2.6.0/) has been modified to include modules that are important when processing RRBS/cfRRBS samples. The pipeline has been modified by @edogiuili and is currently maintained by Edoardo Giuili ([@edogiuili](https://github.com/edogiuili)) and Sofie Van de Velde ([@sofvdvel](https://github.com/sofvdvel)).\n\n### Removal of optical duplicates\n\n#### `--remove_optic_duplicates`\n\nIf specified, it removes the optical duplicates. It can be used together with `--sequencer` (see below).\n\n#### `--sequencer`\n\nIf the flag `--remove_optic_duplicates` has been specified, `--sequencer` will be by default set to **NovaSeq**. Alternatively, you can specify **HiSeq** or **NextSeq**. This will change the OpticalDupsPixelDistance within PicardMarkDuplicates step (**NovaSeq**: 12000, **HiSeq**: 2500, **NextSeq**: 100).\n\n### Filter non conversion (Bismark) module\n\n#### `--filter_non_conversion`\n\nIf specified, it filters out all those reads that have a methylation value \u003e= than a preset threshold in non-CG context where you expect a very low methylation level (\u003c5% usually). For more information please consult the [Bismark usage](https://felixkrueger.github.io/Bismark/bismark/filter_nonconverted_reads/).\n\n#### `--minimum_count`\n\nMinimum number of methylation sites for a read to be filtered out (def. 3).\n\n#### `--percentage_cutoff`\n\nMinimum methylation percentage for a read to be filtered out (def. 90%).\n\n### CpG-level sequencing saturation using methurator\n\n#### `--run_methurator`\n\nIf specified (by default: true), it will run [methurator](https://vibtobilab.github.io/methurator/latest/) to compute a CpG-level sequencing saturation analysis.\n\n#### `--t_max`\n\nMaximum extrapolation factor (t) value (def. 10).\n\n#### `--minimum_coverage`\n\nMinimum number of counts to define a new CpG (def. 1). More than 1 value can be specified (e.g. '1,3,5').\n\n## Pipeline output\n\nTo 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.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/methylseq/output).\n\n## Credits\n\nThese 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.\n\n- Main authors of original nf-core/methylseq pipeline:\n  - Phil Ewels ([@ewels](https://github.com/ewels/))\n- Maintainers:\n  - Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))\n  - Sateesh Peri ([@Sateesh_Peri](https://github.com/sateeshperi))\n  - Edmund Miller ([@EMiller88](https://github.com/emiller88))\n- Contributors:\n  - Rickard Hammarén ([@Hammarn](https://github.com/Hammarn/))\n  - Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))\n  - Patrick Hüther ([@phue](https://github.com/phue/))\n\n## Citations\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvibtobilab%2Fmethylseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvibtobilab%2Fmethylseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvibtobilab%2Fmethylseq/lists"}