radseq
Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 10 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.4%) to scientific vocabulary
Keywords
Repository
Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: dev
- Homepage: https://nf-co.re/radseq
- Size: 2.68 MB
Statistics
- Stars: 7
- Watchers: 176
- Forks: 6
- Open Issues: 2
- Releases: 0
Topics
Metadata Files
README.md
Introduction
nf-core/radseq is a bioinformatics best-practice variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
The pipeline is built using Nextflow, 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. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
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.
Pipeline summary
- Read QC (
FastQC) - Adapter and quality trimming (
FastP) Choice of constructing psuedoreference (i) or using existing reference (ii)
ii. No Preprossesing
Choice of alignment software
i.
BWAii.
BWA-mem2UMI-based deduplicated (
UMI-tools)Index, merge and index alignments (
SAMtools)Construct intervals for freebayes (
BEDtools)Variant calling (
FreeBayes)Present QC for raw reads (
MultiQC)
Quick Start
Install
Nextflow(>=21.10.3)Install any of
Docker,Singularity,Podman,ShifterorCharliecloudfor full pipeline reproducibility (please only useCondaas a last resort; see docs)Download the pipeline and test it on a minimal dataset with a single command:
console nextflow run nf-core/radseq -profile test,YOURPROFILENote that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (
YOURPROFILEin the example command above). You can chain multiple config profiles in a comma-separated string.- The pipeline comes with config profiles called
docker,singularity,podman,shifter,charliecloudandcondawhich instruct the pipeline to use the named tool for software management. For example,-profile test,docker. - Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>in your command. This will enable eitherdockerorsingularityand set the appropriate execution settings for your local compute environment. - If you are using
singularityand are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the--singularity_pull_docker_containerparameter to pull and convert the Docker image instead. Alternatively, you can use thenf-core downloadcommand to download images first, before running the pipeline. Setting theNXF_SINGULARITY_CACHEDIRorsingularity.cacheDirNextflow options enables you to store and re-use the images from a central location for future pipeline runs. - If you are using
conda, it is highly recommended to use theNXF_CONDA_CACHEDIRorconda.cacheDirsettings to store the environments in a central location for future pipeline runs.
- The pipeline comes with config profiles called
Start running your own analysis!
console nextflow run nf-core/radseq -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv
Documentation
The nf-core/radseq pipeline comes with documentation about the pipeline usage, parameters and output.
Credits
dDocent was originally written by Jon Puritz and developed into nf-core/radseq by Gabriel Barrett
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on the Slack #radseq channel (you can join with this invite).
Citations
An extensive list of references for the tools used by the pipeline can be found in the 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.
Owner
- Name: nf-core
- Login: nf-core
- Kind: organization
- Email: core@nf-co.re
- Website: http://nf-co.re
- Twitter: nf_core
- Repositories: 84
- Profile: https://github.com/nf-core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Citation (CITATIONS.md)
# nf-core/radseq: Citations
## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
## [dDocent](https://github.com/jpuritz/dDocent)
> Puritz JB, Hollenbeck CM, Gold JR. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ. 2014 Jun 10;2:e431. doi: 10.7717/peerj.431. Epub 2014 Jun 10. PubMed PMID: 24949246; PubMed Central PMCID: PMC4060032.
## Pipeline tools
- [BEDOPS](https://pubmed.ncbi.nlm.nih.gov/22576172/)
> Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 Jul 15;28(14):1919-20. doi: 10.1093/bioinformatics/bts277. Epub 2012 May 9. PubMed PMID: 22576172. PubMed Central PMCID: PMC3389768.
- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
> Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
- [BCFTools](https://pubmed.ncbi.nlm.nih.gov/21903627/)
> Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575.
- [BWA-MEM](https://arxiv.org/abs/1303.3997v2)
> Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997
* [CD-HIT](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516142/)
> Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012 Dec 1;28(23):3150-2. doi: 10.1093/bioinformatics/bts565. Epub 2012 Oct 11. PubMed PMID: 23060610. PubMed Central PMCID: PMC3516142.
* [FastP](https://pubmed.ncbi.nlm.nih.gov/30423086/)
> Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-90. doi: 10.1093/bioinformatics/bty560. PubMed PMID: PMC6129281. PubMed Central PMCID: 30423086.
* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
- [FreeBayes](https://arxiv.org/abs/1207.3907)
> Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907
* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
- [Rainbow](https://academic.oup.com/bioinformatics/article/28/21/2732/233132)
> Li YL, Xue DX, Zhang BD, Liu JX. An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals. Royal Society Open Science. 2018 Feb 28;5(2):171589. doi: 10.1098/rsos.171589. Epub 2018 Feb 28. PubMed PMID: 29515871. PubMed Central PMCID: PMC5830760.
- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
> Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
- [SeqKit](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051824/)
> Shen W, Le S, Li Y, Hu F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS one. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PubMed PMID: 27706213. PubMed Central PMCID: PMC5051824.
- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)
> Li H, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982. PubMed Central PMCID: PMC3042176.
- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
> Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.
## Software packaging/containerisation tools
* [Anaconda](https://anaconda.com)
> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
GitHub Events
Total
- Watch event: 1
- Issue comment event: 12
- Push event: 5
- Pull request event: 12
- Fork event: 1
- Create event: 6
Last Year
- Watch event: 1
- Issue comment event: 12
- Push event: 5
- Pull request event: 12
- Fork event: 1
- Create event: 6
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gabriel-A-Barrett | g****t@u****u | 77 |
| Gabe Barrett | 6****t@u****m | 11 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 9
- Average time to close issues: about 1 month
- Average time to close pull requests: about 2 months
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.67
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 2 months
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.4
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Gabriel-A-Barrett (3)
Pull Request Authors
- nf-core-bot (18)
- Gabriel-A-Barrett (2)
- ewels (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- nf-core/tower-action v2 composite
- nf-core/tower-action v2 composite
- mshick/add-pr-comment v1 composite
- actions/checkout v2 composite
- actions/checkout v3 composite
- actions/setup-node v3 composite
- actions/setup-python v4 composite
- actions/upload-artifact v3 composite
- mshick/add-pr-comment v1 composite
- nf-core/setup-nextflow v1 composite
- psf/black stable composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite