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grenedalf

Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments

https://github.com/lczech/grenedalf

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
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.2%) to scientific vocabulary

Keywords

allele-frequencies evolve-and-resequence pool-sequencing poolfstat popoolation popoolation2 population-genetics
Last synced: 6 months ago · JSON representation ·

Repository

Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments

Basic Info
  • Host: GitHub
  • Owner: lczech
  • License: gpl-3.0
  • Language: C++
  • Default Branch: master
  • Homepage:
  • Size: 19.2 MB
Statistics
  • Stars: 42
  • Watchers: 3
  • Forks: 4
  • Open Issues: 7
  • Releases: 11
Topics
allele-frequencies evolve-and-resequence pool-sequencing poolfstat popoolation popoolation2 population-genetics
Created over 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

Bioconda install Downloads Release Language Softwipe Score CI License DOI <!-- CI --> <!-- Platforms --> <!-- Build Status -->

grenedalf

Features

grenedalf is a collection of commands for working with pool sequencing population genetic data. Its main focus are statistical analyses such as Tajima's D and Fst, as well as convenience functions around pool sequencing data. The statistics follow the approaches of PoPoolation and PoPoolation2, as well as poolfstat and npstat. However, compared to those, grenedalf is significantly more scalable, more user friendly, and offers more settings and input file formats.

Setup

We recommend to first try the pre-compiled binaries of the latest Release, by downloading the binary for your system from the "Assets" list below the release. Alternatively, grenedalf can be installed via bioconda. If that does not work, it can be build from source as described here. If you want the best performance, we recommend to build from source anyway.

Usage and Documentation

grenedalf is used via its command line interface, with commands for each task. The commands have the general structure: <!-- grenedalf -->

grenedalf <command> <options>

See the Wiki pages for the list of all commands and their documentation.

Support and Requests

For questions, bug reports, and feature requests, please 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 here where they can be found.

Feedback on functionality, interface, and features is highly appreciated, as we are always open to discussing new statistics and tools that might be relevant for the community. If you need other pool sequencing statistics than the ones already offered here, please reach out - happy to explore the potential for a collaboration there! We have a lot of code infrastructure in grenedalf that takes care of all the basics, and so it would be nice to implement further statistics!

Citation

Please find the publication here:

grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
Bioinformatics, 2024. doi:10.1093/bioinformatics/btae508

Each command also prints out the relevant references for that command. Then, the command grenedalf citation can be used to obtain details on those references.

Owner

  • Name: Lucas Czech
  • Login: lczech
  • Kind: user
  • Location: Stanford, USA
  • Company: Carnegie Institution for Science

Postdoc in bioinformatics :seedling: and computer scientist :octocat: working on inter-disciplinary ways to save the planet :earth_africa:

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: "Spence"
    given-names: "Jeffrey P"
    orcid: "https://orcid.org/0000-0002-3199-1447"
  - family-names: "Expósito-Alonso"
    given-names: "Moisés"
    orcid: "https://orcid.org/0000-0001-5711-0700"
title: "grenedalf: population genetic statistics for the next generation of pool sequencing"
doi: 10.1093/bioinformatics/btae508
url: https://doi.org/10.1093/bioinformatics/btae508
preferred-citation:
  authors:
    - family-names: "Czech"
      given-names: "Lucas"
      orcid: "https://orcid.org/0000-0002-1340-9644"
    - family-names: "Spence"
      given-names: "Jeffrey P"
      orcid: "https://orcid.org/0000-0002-3199-1447"
    - family-names: "Expósito-Alonso"
      given-names: "Moisés"
      orcid: "https://orcid.org/0000-0001-5711-0700"
  title: "grenedalf: population genetic statistics for the next generation of pool sequencing"
  doi: 10.1093/bioinformatics/btae508
  url: https://doi.org/10.1093/bioinformatics/btae508
  type: article-journal
  journal: "Bioinformatics"
  pages: btae508
  year: 2024
  volume: 40
  issue: 8

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 10
  • Watch event: 8
  • Issue comment event: 44
  • Push event: 8
  • Gollum event: 1
  • Fork event: 2
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 10
  • Watch event: 8
  • Issue comment event: 44
  • Push event: 8
  • Gollum event: 1
  • Fork event: 2

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 354
  • Total Committers: 1
  • Avg Commits per committer: 354.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 51
  • Committers: 1
  • Avg Commits per committer: 51.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lucas Czech l****h@g****m 354

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 43
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 34
  • Total pull request authors: 0
  • Average comments per issue: 5.51
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 0
  • Average time to close issues: 15 days
  • Average time to close pull requests: N/A
  • Issue authors: 12
  • Pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • capoony (5)
  • vilperte (3)
  • SheepwormJM (2)
  • biozzq (2)
  • mhoban (2)
  • plunkert (1)
  • douglasgscofield (1)
  • VitoriaHorvathMiranda (1)
  • GaloGS (1)
  • tiphaine-b (1)
  • jkreinz (1)
  • Easybel (1)
  • ribeirots (1)
  • ospfsg (1)
  • peterdfields (1)
Pull Request Authors
Top Labels
Issue Labels
question (3) enhancement (2) help wanted (1)
Pull Request Labels

Dependencies

.github/workflows/ci.yaml actions
  • actions/checkout v3.1.0 composite
  • aminya/setup-cpp v0.22.0 composite