nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations]
Crosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists’ toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-based experimental protocols, as well as computat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wellcome
2023-07-01
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| Series: | Wellcome Open Research |
| Subjects: | |
| Online Access: | https://wellcomeopenresearch.org/articles/8-286/v1 |
| _version_ | 1797662198705684480 |
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| author | Charlotte West Chris Cheshire Charlotte Capitanchik Nicholas M. Luscombe Anob Chakrabarti Jernej Ule |
| author_facet | Charlotte West Chris Cheshire Charlotte Capitanchik Nicholas M. Luscombe Anob Chakrabarti Jernej Ule |
| author_sort | Charlotte West |
| collection | DOAJ |
| description | Crosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists’ toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Consequently, there is an urgent need for a well-documented bioinformatic pipeline that enshrines the principles of robustness, reproducibility, scalability, portability and flexibility while embracing the diversity of experimental and computational CLIP tools. To address this, we present nf-core/clipseq - a robust Nextflow pipeline for quality control and analysis of CLIP sequencing data. It is part of the international nf-core community effort to develop and curate a best-practice, gold-standard set of pipelines for data analysis. The standards enabled by Nextflow and nf-core, including workflow management, version control, continuous integration and containerisation ensure that these key needs are met. Furthermore, multiple tools are implemented (e.g. for peak-calling), alongside visualisation of quality control metrics to empower the user to make their own informed decisions based on their data. nf-core/clipseq remains under active development, with plans to incorporate newly released tools to ensure that pipeline remains up-to-date and relevant for the community. Engagement with users and developers is encouraged through the nf-core GitHub repository and Slack channel to promote collaboration. It is available at https://nf-co.re/clipseq. |
| first_indexed | 2024-03-11T18:55:43Z |
| format | Article |
| id | doaj.art-92bb60edcbc54ba9b5f6f394a914bf6a |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-03-11T18:55:43Z |
| publishDate | 2023-07-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-92bb60edcbc54ba9b5f6f394a914bf6a2023-10-11T01:00:01ZengWellcomeWellcome Open Research2398-502X2023-07-01821549nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations]Charlotte West0Chris Cheshire1Charlotte Capitanchik2Nicholas M. Luscombe3Anob Chakrabarti4https://orcid.org/0000-0002-6841-5718Jernej Ule5https://orcid.org/0000-0002-2452-4277The Francis Crick Institute, London, England, UKThe Francis Crick Institute, London, England, UKThe Francis Crick Institute, London, England, UKThe Francis Crick Institute, London, England, UKThe Francis Crick Institute, London, England, UKThe Francis Crick Institute, London, England, UKCrosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists’ toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Consequently, there is an urgent need for a well-documented bioinformatic pipeline that enshrines the principles of robustness, reproducibility, scalability, portability and flexibility while embracing the diversity of experimental and computational CLIP tools. To address this, we present nf-core/clipseq - a robust Nextflow pipeline for quality control and analysis of CLIP sequencing data. It is part of the international nf-core community effort to develop and curate a best-practice, gold-standard set of pipelines for data analysis. The standards enabled by Nextflow and nf-core, including workflow management, version control, continuous integration and containerisation ensure that these key needs are met. Furthermore, multiple tools are implemented (e.g. for peak-calling), alongside visualisation of quality control metrics to empower the user to make their own informed decisions based on their data. nf-core/clipseq remains under active development, with plans to incorporate newly released tools to ensure that pipeline remains up-to-date and relevant for the community. Engagement with users and developers is encouraged through the nf-core GitHub repository and Slack channel to promote collaboration. It is available at https://nf-co.re/clipseq.https://wellcomeopenresearch.org/articles/8-286/v1CLIP Nextflow RNA-protein interactions peak calling reproducible research bioinformatic pipelineseng |
| spellingShingle | Charlotte West Chris Cheshire Charlotte Capitanchik Nicholas M. Luscombe Anob Chakrabarti Jernej Ule nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] Wellcome Open Research CLIP Nextflow RNA-protein interactions peak calling reproducible research bioinformatic pipelines eng |
| title | nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] |
| title_full | nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] |
| title_fullStr | nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] |
| title_short | nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis [version 1; peer review: 1 approved, 2 approved with reservations] |
| title_sort | nf core clipseq a robust nextflow pipeline for comprehensive clip data analysis version 1 peer review 1 approved 2 approved with reservations |
| topic | CLIP Nextflow RNA-protein interactions peak calling reproducible research bioinformatic pipelines eng |
| url | https://wellcomeopenresearch.org/articles/8-286/v1 |
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