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eukrep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

https://github.com/patrickwest/eukrep

Science Score: 23.0%

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

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    2 of 4 committers (50.0%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Basic Info
  • Host: GitHub
  • Owner: patrickwest
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 3.2 MB
Statistics
  • Stars: 71
  • Watchers: 2
  • Forks: 12
  • Open Issues: 14
  • Releases: 0
Created about 9 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Installation

  • Requires Python3
  • Install with conda (recommended) $ conda create -y -n eukrep-env -c bioconda scikit-learn==0.19.2 eukrep
  • Install with pip (requires scikit-learn v 0.19.2) $ pip install EukRep # Example Usage #
  • Identify and output sequences predicted to be of eukaryotic origin from a fasta file: $ EukRep -i <Sequences in Fasta format> -o <Eukaryote sequence output file>
  • Identify and output both sequences of eukaryotic and prokaryotic origin from a fasta file: $ EukRep -i <Sequences in Fasta format> -o <Eukaryote sequence output file> --prokarya <Prokaryote sequence output file>

Obtaining Eukaryotic Bins

EukRep is intended to be used as one part of a larger pipeline. For obtaining high quality gene predictions and binning identified eukaryotic contigs as described in "Genome-reconstruction for eukaryotes from complex natural microbial communities" (West et al. in review), see methods section https://doi.org/10.1101/171355

-or-

See a provided example workflow (work in progess) https://github.com/patrickwest/EukRep_Pipeline

Adjusting Stringency

The stringency of identifying eukaryotic contigs can be adjusted with -m. The false positive rate (FPR) and false negative rate (FNR) for the strict, balanced, and lenient modes are shown below. Default is balanced. Prior to version 0.6.5, lenient was the default.

20kb

5kb

Data was obtained by running EukRep on 20kb and 5kb fragmented scaffolds from genomes from mock novel phyla.

Important Caveat

In our experience, most metagenomes do not have a eukaryotic genome present; however, EukRep has a false positive rate and you will still receive output in these cases.

Owner

  • Name: Patrick T West
  • Login: patrickwest
  • Kind: user

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 49
  • Total Committers: 4
  • Avg Commits per committer: 12.25
  • Development Distribution Score (DDS): 0.061
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Patrick T West p****t@b****u 46
Marcus Fedarko m****o@u****u 1
root r****t@L****n 1
Ben J Woodcroft d****n@g****m 1
Committer Domains (Top 20 + Academic)
laptop-9esib35g.localdomain: 1 umd.edu: 1 berkeley.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 20
  • Total pull requests: 4
  • Average time to close issues: 6 months
  • Average time to close pull requests: 7 months
  • Total issue authors: 17
  • Total pull request authors: 4
  • Average comments per issue: 1.4
  • Average comments per pull request: 0.25
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • jolespin (3)
  • tseemann (2)
  • AmaliT (1)
  • fredchaux (1)
  • Ahmed-Shibl (1)
  • li0604 (1)
  • wwood (1)
  • ilarioferrocino (1)
  • susheelbhanu (1)
  • apcamargo (1)
  • weiguanyue (1)
  • jzrapp (1)
  • mgabriell1 (1)
  • FengqingWang0712 (1)
  • rotoscan (1)
Pull Request Authors
  • dependabot[bot] (2)
  • wwood (1)
  • fedarko (1)
  • lfdelzam (1)
Top Labels
Issue Labels
question (6) bug (1)
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 40 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 1
pypi.org: eukrep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 40 Last month
Rankings
Stargazers count: 8.6%
Dependent packages count: 10.0%
Forks count: 10.2%
Average: 15.9%
Dependent repos count: 21.7%
Downloads: 29.1%
Maintainers (1)
patrickwest
Last synced: 11 months ago

Dependencies

EukRep.egg-info/requires.txt pypi
  • biopython *
  • kpal *
  • numpy *
  • scikit-learn *
setup.py pypi
  • biopython *
  • kpal *
  • numpy *
  • scikit-learn *