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grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

https://github.com/moiexpositoalonsolab/grenepipe

Science Score: 57.0%

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 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary

Keywords

ancient-dna evolve-and-resequence genomic-variant-calling pool-sequencing population-genetics snakemake snakemake-workflow variant-calling variant-calls
Last synced: 6 months ago · JSON representation ·

Repository

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

Basic Info
  • Host: GitHub
  • Owner: moiexpositoalonsolab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage: http://grene-net.org
  • Size: 100 MB
Statistics
  • Stars: 101
  • Watchers: 3
  • Forks: 23
  • Open Issues: 2
  • Releases: 24
Topics
ancient-dna evolve-and-resequence genomic-variant-calling pool-sequencing population-genetics snakemake snakemake-workflow variant-calling variant-calls
Created almost 6 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

Snakemake CI Platforms Release License DOI <!-- CI --> <!-- Language -->

grenepipe logo

Snakemake workflow for variant calling from raw sample sequences, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

Advantages:

  • One command to run the whole pipeline!
  • Many tools to choose from for each step
  • Simple configuration via a single file
  • Automatic download of tool dependencies
  • Resuming from failing jobs

Getting Started

See --> the Wiki pages <-- for setup and documentation.

For questions, bug reports, and feature requests, open an issue. Please do not send emails with questions or requests, as others might be having them as well, and so it is better to discuss them where they can be found.

Pipeline Overview

Minimal input:

  • Reference genome fasta file
  • Per-sample fastq files
  • Optionally, a vcf file of known variants to restrict the variant calling process

Process and available tools:

Typical output:

  • Variant calls vcf, raw and filtered, and potentially with annotations
  • MultiQC report (includes summaries of most other tools, and of the final vcf)
  • Snakemake report (optional)

Intermediate output files such as bam files are also kept by default, and mpileup files can optionally be created if needed. In addition to the above tools, there are some tools used as glue between the steps. If you are interested in the details, have a look at the snakemake rules for each step.

Citation

When using grenepipe, please cite:

grenepipe: A flexible, scalable, and reproducible pipeline
to automate variant calling from sequence reads.
Lucas Czech and Moises Exposito-Alonso. Bioinformatics. 2022.
doi:10.1093/bioinformatics/btac600 [pdf]

Furthermore, please do not forget to cite all tools that you selected to be run for your analysis. See our Wiki for their references.

Owner

  • Name: moilab
  • Login: moiexpositoalonsolab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
authors:
- family-names: "Czech"
  given-names: "Lucas"
  orcid: "https://orcid.org/0000-0002-1340-9644"
- family-names: "Exposito-Alonso"
  given-names: "Moises"
  orcid: "https://orcid.org/0000-0001-5711-0700"
title: "grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads"
doi: 10.1093/bioinformatics/btac600
url: "https://github.com/moiexpositoalonsolab/grenepipe"
preferred-citation:
  type: article
  authors:
  - family-names: "Czech"
    given-names: "Lucas"
    orcid: "https://orcid.org/0000-0002-1340-9644"
  - family-names: "Exposito-Alonso"
    given-names: "Moises"
    orcid: "https://orcid.org/0000-0001-5711-0700"
  doi: "10.1093/bioinformatics/btac600"
  journal: "Bioinformatics"
  start: 4809 # First page number
  end: 4811 # Last page number
  title: "grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads"
  volume: 38
  issue: 20
  year: 2022

GitHub Events

Total
  • Create event: 5
  • Release event: 5
  • Issues event: 25
  • Watch event: 13
  • Issue comment event: 81
  • Push event: 38
  • Gollum event: 10
  • Fork event: 2
Last Year
  • Create event: 5
  • Release event: 5
  • Issues event: 25
  • Watch event: 13
  • Issue comment event: 81
  • Push event: 38
  • Gollum event: 10
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 9
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 7
  • Total pull request authors: 0
  • Average comments per issue: 4.89
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 7
  • Pull request authors: 0
  • Average comments per issue: 4.89
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
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Issue Authors
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Pull Request Authors
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Issue Labels
enhancement (1)
Pull Request Labels

Dependencies

.github/workflows/ci.yaml actions
  • actions/checkout v3.1.0 composite
  • actions/upload-artifact v3 composite
  • conda-incubator/setup-miniconda v2.2.0 composite
.github/workflows/snakefmt.yml_ actions
  • actions/checkout v2 composite
  • github/super-linter v3 composite
pyproject.toml pypi