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paleomix

Pipelines and tools for the processing of ancient and modern HTS data.

https://github.com/mikkelschubert/paleomix

Science Score: 59.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Pipelines and tools for the processing of ancient and modern HTS data.

Basic Info
Statistics
  • Stars: 47
  • Watchers: 5
  • Forks: 20
  • Open Issues: 9
  • Releases: 28
Created over 13 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.rst 

**********************
The PALEOMIX pipelines
**********************

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

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Installation and usage
----------------------

Detailed instructions can be found in the `documentation `_ for PALEOMIX. For questions, bug reports, and/or suggestions, please use the `GitHub tracker `_ or contact Mikkel Schubert at `MikkelSch@gmail.com `_.


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Citations
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The PALEOMIX pipelines have been published in Nature Protocols; if you make use of PALEOMIX in your work, then please cite

  Schubert M, Ermini L, Sarkissian CD, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, and Orlando L. "**Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX**". Nat Protoc. 2014 May;9(5):1056-82. doi: `10.1038/nprot.2014.063 `_. Epub 2014 Apr 10. PubMed PMID: `24722405 `_.

The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite

  Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2017 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 `_.


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Related tools
-------------

* `DamMet `_: Probabilistic modelling of ancient methylomes using sequencing data underlying an ancient specimen.
* `gargammel `_: Simulations of ancient DNA datasets.
* `mapDamage `_: Tracking and quantifying damage patterns in ancient DNA sequences.
* `nf-core/eager `_: A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

Owner

  • Name: Mikkel Schubert
  • Login: MikkelSchubert
  • Kind: user

GitHub Events

Total
  • Create event: 19
  • Release event: 2
  • Issues event: 5
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 11
  • Push event: 22
  • Pull request event: 33
  • Fork event: 1
Last Year
  • Create event: 19
  • Release event: 2
  • Issues event: 5
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 11
  • Push event: 22
  • Pull request event: 33
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 2,115
  • Total Committers: 7
  • Avg Commits per committer: 302.143
  • Development Distribution Score (DDS): 0.075
Past Year
  • Commits: 71
  • Committers: 1
  • Avg Commits per committer: 71.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mikkel Schubert M****h@g****m 1,956
Mikkel Schubert 2****t 145
Mikkel Schubert m****h@b****k 10
Aurelien Ginolhac g****c@g****m 1
Graham Gower g****r@g****m 1
beeso018 b****8@u****u 1
jfy133 j****3@g****m 1
Committer Domains (Top 20 + Academic)
umn.edu: 1 biosustain.dtu.dk: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 58
  • Total pull requests: 20
  • Average time to close issues: 4 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 43
  • Total pull request authors: 4
  • Average comments per issue: 3.74
  • Average comments per pull request: 0.15
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 16
  • Average time to close issues: 4 days
  • Average time to close pull requests: 4 days
  • Issue authors: 6
  • Pull request authors: 1
  • Average comments per issue: 4.17
  • Average comments per pull request: 0.06
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • tillea (4)
  • flaviode (2)
  • grahamgower (2)
  • Rhinogradentia (2)
  • sagitaninta (2)
  • laurenhamm (2)
  • gtrichard (2)
  • nwales (2)
  • ginolhac (2)
  • jfy133 (2)
  • Uriwolkow (1)
  • xuefenfei712 (1)
  • ArchaeologyRoz (1)
  • beeso018 (1)
  • schae234 (1)
Pull Request Authors
  • MikkelSchubert (34)
  • ginolhac (1)
  • jfy133 (1)
  • grahamgower (1)
Top Labels
Issue Labels
question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 111 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 33
  • Total maintainers: 1
pypi.org: paleomix

Bioinformatics pipelines for HTS data

  • Versions: 33
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 111 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 1.5%
Forks count: 8.7%
Dependent repos count: 9.0%
Average: 9.9%
Dependent packages count: 10.0%
Stargazers count: 10.2%
Downloads: 19.8%
Maintainers (1)
mischu
Last synced: 10 months ago

Dependencies

setup.py pypi
  • coloredlogs >=10.0
  • configargparse >=0.13.0
  • humanfriendly >=4.7
  • packaging >=19.0
  • pysam >=0.10.0
  • ruamel.yaml >=0.16.0
  • setproctitle >=1.1.0