sequencecomposition
Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
Science Score: 65.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓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
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○Academic email domains
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✓Institutional organization owner
Organization sanger-tol has institutional domain (www.sanger.ac.uk) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
Keywords
Repository
Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
Basic Info
- Host: GitHub
- Owner: sanger-tol
- License: mit
- Language: Groovy
- Default Branch: main
- Homepage: https://pipelines.tol.sanger.ac.uk/sequencecomposition
- Size: 2.91 MB
Statistics
- Stars: 2
- Watchers: 6
- Forks: 2
- Open Issues: 20
- Releases: 2
Topics
Metadata Files
README.md
Introduction
sanger-tol/sequencecomposition is a bioinformatics analysis pipeline that extracts statistics from a genome about its sequence composition.
The pipeline takes an assembly Fasta file (possibly compressed), runs fasta_windows on it, and transforms the outputs into files more practical for downstream use.
Steps involved:
- Run
fasta_windowson the assembly Fasta file. - Extract single-statistics bedGraph files from the multi-statistics TSV
files
fasta_windowsoutputs. - Compress and index all bedGraph and TSV files with
bgzipandtabix.
Usage
Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with
-profile testbefore running the workflow on actual data.
The easiest is to provide the path of the Fasta file to analyse like this:
console
nextflow run sanger-tol/sequencecomposition --fasta /path/to/genome.fa
Warning: Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs.
The pipeline also supports bulk downloads through a sample-sheet. More information about this mode on our pipeline website.
Credits
sanger-tol/sequencecomposition was originally written by Matthieu Muffato.
We thank the following people for their assistance in the development of this pipeline:
- Priyanka Surana for providing reviews.
- Tyler Chafin for updates.
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 #pipelines channel. Please create an issue on GitHub if you are not on the Sanger slack channel.
Citations
If you use sanger-tol/sequencecomposition for your analysis, please cite it using the following doi: 10.5281/zenodo.14358108
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
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: Tree of Life programme
- Login: sanger-tol
- Kind: organization
- Location: United Kingdom
- Website: https://www.sanger.ac.uk/programme/tree-of-life/
- Twitter: sangertol
- Repositories: 15
- Profile: https://github.com/sanger-tol
The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: sanger-tol/sequencecomposition
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Matthieu
family-names: Muffato
affiliation: Wellcome Sanger Institute
orcid: "https://orcid.org/0000-0002-7860-3560"
- given-names: Priyanka
family-names: Surana
orcid: "https://orcid.org/0000-0002-7167-0875"
affiliation: Wellcome Sanger Institute
- given-names: Tyler
family-names: Chafin
orcid: "https://orcid.org/0000-0001-8687-5905"
affiliation: Wellcome Sanger Institute
identifiers:
- type: doi
value: 10.5281/zenodo.14358108
repository-code: "https://github.com/sanger-tol/sequencecomposition"
license: MIT
commit: TODO
version: 2.0.0
date-released: "2022-10-08"
GitHub Events
Total
- Create event: 7
- Release event: 1
- Issues event: 2
- Delete event: 8
- Member event: 1
- Issue comment event: 18
- Push event: 27
- Pull request review event: 7
- Pull request event: 14
- Fork event: 2
Last Year
- Create event: 7
- Release event: 1
- Issues event: 2
- Delete event: 8
- Member event: 1
- Issue comment event: 18
- Push event: 27
- Pull request review event: 7
- Pull request event: 14
- Fork event: 2
Dependencies
- mshick/add-pr-comment v1 composite
- actions/checkout v2 composite
- nf-core/setup-nextflow v1 composite
- actions/checkout v3 composite
- actions/setup-node v2 composite
- actions/checkout v2 composite
- actions/setup-node v2 composite
- actions/setup-python v3 composite
- actions/upload-artifact v2 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
- actions/stale v7 composite
- actions/upload-artifact v3 composite
- seqeralabs/action-tower-launch v2 composite
- actions/upload-artifact v3 composite
- seqeralabs/action-tower-launch v2 composite