{"id":24186558,"url":"https://github.com/drpatelh/nf-core-sgrnaquant","last_synced_at":"2026-03-07T06:02:54.359Z","repository":{"id":119783525,"uuid":"211314477","full_name":"drpatelh/nf-core-sgrnaquant","owner":"drpatelh","description":"UNDER CONSTRUCTION: CRISPR sgRNA quantification pipeline","archived":false,"fork":false,"pushed_at":"2019-09-27T16:32:35.000Z","size":66,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-03T01:42:17.260Z","etag":null,"topics":["counting","crispr","crispr-analysis","nextflow","nf-core","pipeline","quantification","sgrna","workflow"],"latest_commit_sha":null,"homepage":"http://nf-co.re","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/drpatelh.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-09-27T12:28:53.000Z","updated_at":"2019-09-27T16:49:03.000Z","dependencies_parsed_at":null,"dependency_job_id":"37200b7d-f97e-4617-8257-61149cb10f2f","html_url":"https://github.com/drpatelh/nf-core-sgrnaquant","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/drpatelh/nf-core-sgrnaquant","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-sgrnaquant","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-sgrnaquant/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-sgrnaquant/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-sgrnaquant/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/drpatelh","download_url":"https://codeload.github.com/drpatelh/nf-core-sgrnaquant/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drpatelh%2Fnf-core-sgrnaquant/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30208802,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-07T05:23:27.321Z","status":"ssl_error","status_checked_at":"2026-03-07T05:00:17.256Z","response_time":53,"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":["counting","crispr","crispr-analysis","nextflow","nf-core","pipeline","quantification","sgrna","workflow"],"created_at":"2025-01-13T12:36:04.556Z","updated_at":"2026-03-07T06:02:54.333Z","avatar_url":"https://github.com/drpatelh.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ![nf-core/sgrnaquant](docs/images/nfcore-sgrnaquant_logo.png)\n\n[![Build Status](https://travis-ci.com/nf-core/sgrnaquant.svg?branch=master)](https://travis-ci.com/nf-core/sgrnaquant)\n[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)\n\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)\n[![Docker](https://img.shields.io/docker/automated/nfcore/sgrnaquant.svg)](https://hub.docker.com/r/nfcore/sgrnaquant)\n\n## Introduction\n\n**nfcore/sgrnaquant** is a bioinformatics analysis pipeline used for the quantification of CRISPR sgRNA guides obtained from Illumina sequencing.\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 comes with docker containers making installation trivial and results highly reproducible.\n\n## Pipeline summary\n\n1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter trimming ([`cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html))\n3. Alignment ([`BWA`](https://sourceforge.net/projects/bio-bwa/files/))\n4. Count reads and split by strand after filtering ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html) to remove:\n    1. reads that are unmapped\n    2. reads that map to multiple guides\n    3. reads containing \u003e 0 mismatches\n5. Present QC for raw read, alignment and filtering results ([`MultiQC`](http://multiqc.info/))\n\n## Quick Start\n\ni. Install [`nextflow`](https://nf-co.re/usage/installation)\n\nii. Install one of [`docker`](https://docs.docker.com/engine/installation/), [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`conda`](https://conda.io/miniconda.html)\n\niii. Download the pipeline and test it on a minimal dataset with a single command\n\n```bash\nnextflow run nf-core/sgrnaquant -profile test,\u003cdocker/singularity/conda\u003e\n```\n\niv. Start running your own analysis!\n\n```bash\nnextflow run nf-core/sgrnaquant -profile \u003cdocker/singularity/conda\u003e --design design.csv\n```\n\nSee [usage docs](docs/usage.md) for all of the available options when running the pipeline.\n\n## Documentation\n\nThe nf-core/sgrnaquant pipeline comes with documentation about the pipeline, found in the `docs/` directory:\n\n1. [Installation](https://nf-co.re/usage/installation)\n2. Pipeline configuration\n    * [Local installation](https://nf-co.re/usage/local_installation)\n    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)\n3. [Running the pipeline](docs/usage.md)\n4. [Output and how to interpret the results](docs/output.md)\n5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)\n\n## Credits\n\nThe pipeline was originally written by [The Bioinformatics \u0026 Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London.\n\nThe pipeline was developed by [Harshil Patel](mailto:harshil.patel@crick.ac.uk).\n\n## Citation\n\n\u003c!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. --\u003e\n\u003c!-- If you use nf-core/sgrnaquant for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\nYou can cite the `nf-core` pre-print as follows:  \nEwels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrpatelh%2Fnf-core-sgrnaquant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdrpatelh%2Fnf-core-sgrnaquant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrpatelh%2Fnf-core-sgrnaquant/lists"}