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PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA

PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA - Published in JOSS (2026)

https://github.com/stschiff/sequencetools

Science Score: 87.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic links in README
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    Academic email domains
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    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: about 2 months ago · JSON representation

JOSS Publication

PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA
Published
May 05, 2026
DOI
Volume 11, Issue 121, Page 8634
Authors
Stephan Schiffels ORCID
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Editor
AHM Mahfuzur Rahman ORCID
Tags
Ancient DNA Genome Sequencing Bioinformatics
View PDF Review Thread Software Archive

Issues and Pull Requests

Last synced: 3 months ago

All Time
  • Total issues: 31
  • Total pull requests: 9
  • Average time to close issues: 6 months
  • Average time to close pull requests: 21 days
  • Total issue authors: 20
  • Total pull request authors: 4
  • Average comments per issue: 3.74
  • Average comments per pull request: 1.89
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: 23 days
  • Average time to close pull requests: about 1 month
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 5.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • stschiff (6)
  • npsonis (3)
  • juhp (2)
  • mscbig (2)
  • teepean (2)
  • TCLamnidis (2)
  • KovachLab (1)
  • thomasisensee (1)
  • batelz (1)
  • Arkkienkeli (1)
  • apeltzer (1)
  • SRgen (1)
  • idiltac (1)
  • mnievesc (1)
  • sc13-bioinf (1)
Pull Request Authors
  • stschiff (4)
  • teepean (2)
  • sequencetoolsconda (2)
  • apeltzer (1)
Top Labels
Issue Labels
enhancement (3) wontfix (1) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • hackage 2,897 total
  • Total dependent packages: 1
  • Total dependent repositories: 7
  • Total versions: 9
  • Total maintainers: 1
hackage.haskell.org: sequenceTools

The tools in this package process sequencing Data, in particular from ancient DNA sequencing libraries. Key tool in this package is pileupCaller, a tool to randomly sample genotypes from sequencing data.

  • Versions: 9
  • Dependent Packages: 1
  • Dependent Repositories: 7
  • Downloads: 2,897 Total
Rankings
Dependent packages count: 10.5%
Forks count: 12.2%
Stargazers count: 13.5%
Average: 21.4%
Dependent repos count: 21.5%
Downloads: 49.3%
Maintainers (1)
stephan_schiffels
Last synced: 2 months ago