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kevlar

Reference-free variant discovery in large eukaryotic genomes

https://github.com/kevlar-dev/kevlar

Science Score: 41.0%

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.1%) to scientific vocabulary

Keywords

dna genome-variation genomics variant-calling
Last synced: 4 months ago · JSON representation ·

Repository

Reference-free variant discovery in large eukaryotic genomes

Basic Info
Statistics
  • Stars: 41
  • Watchers: 4
  • Forks: 9
  • Open Issues: 23
  • Releases: 0
Topics
dna genome-variation genomics variant-calling
Created about 9 years ago · Last pushed over 4 years ago
Metadata Files
Readme Changelog License Citation

README.md

kevlar build status PyPI version Test coverage kevlar documentation Docker build status MIT licensed

What if I told you we don't need alignments to find variants?

kevlar

Daniel Standage, 2016-2019
https://kevlar.readthedocs.io

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model. This software is free for use under the MIT license.

Where can I find kevlar online?
  • Source repository: https://github.com/kevlar-dev/kevlar
  • Documentation: https://kevlar.readthedocs.io
  • Stable releases: https://github.com/kevlar-dev/kevlar/releases
  • Issue tracker: https://github.com/kevlar-dev/kevlar/issues
If you have questions or need help with kevlar, the [GitHub issue tracker](https://github.com/kevlar-dev/kevlar) should be your first point of contact.
How do I install kevlar? See [the kevlar documentation](http://kevlar.readthedocs.io/en/latest/install.html) for complete instructions, but the impatient can try the following. ``` pip3 install git+https://github.com/dib-lab/khmer.git pip3 install biokevlar ```
How do I use kevlar?
  • Installation instructions: http://kevlar.readthedocs.io/en/latest/install.html
  • Quick start guide: http://kevlar.readthedocs.io/en/latest/quick-start.html
  • Tutorial: http://kevlar.readthedocs.io/en/latest/tutorial.html
How do I cite kevlar? Standage DS, Brown CT, Hormozdiari F (2019) Kevlar: a mapping-free framework for accurate discovery of de novo variants. *bioRxiv*, [doi:10.1101/549154](https://doi.org/10.1101/549154).
How can I contribute? We welcome contributions to the kevlar project from the community! If you're interested in modifying kevlar or contributing to its ongoing development, feel free to send us a message or submit a pull request! The kevlar software is a project of the [Lab for Data Intensive Biology](http://ivory.idyll.org/lab/) and the [Computational Genomics Lab](http://www.hormozdiarilab.org/) at UC Davis.

Owner

  • Name: kevlar-dev
  • Login: kevlar-dev
  • Kind: organization

Citation (CITATION) 

Standage DS, Brown CT, Hormozdiari F (2019) Kevlar: a mapping-free framework for accurate discovery of de novo variants. bioRxiv, doi:10.1101/549154.

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 850
  • Total Committers: 3
  • Avg Commits per committer: 283.333
  • Development Distribution Score (DDS): 0.033
Top Committers
Name Email Commits
Daniel Standage d****e@g****m 822
Daniel Standage d****e@n****v 27
Sichong Peng s****g@u****u 1
Committer Domains (Top 20 + Academic)
ucdavis.edu: 1 nbacc.dhs.gov: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 54
  • Total pull requests: 46
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 2 days
  • Total issue authors: 12
  • Total pull request authors: 1
  • Average comments per issue: 1.43
  • Average comments per pull request: 1.09
  • Merged pull requests: 45
  • Bot issues: 0
  • Bot pull requests: 0
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
  • standage (35)
  • serosko (3)
  • ghost (3)
  • 17tranap (3)
  • moldach (2)
  • exeter-matthew-wakeling (2)
  • sph17 (1)
  • tseemann (1)
  • blajoie (1)
  • mvelinder (1)
  • pkothiyal (1)
  • ashenflower (1)
Pull Request Authors
  • standage (46)
Top Labels
Issue Labels
bug (10) accuracy (9) enhancement (7) refactoring (4) optimization (4) documentation (2) wontfix (1)
Pull Request Labels
enhancement (11) bug (10) accuracy (10) documentation (5) refactoring (5) optimization (5) configuration (1)

Dependencies

docs/requirements.txt pypi
  • intervaltree >=3.0.2
  • matplotlib *
  • networkx >=2.0
  • pandas *
  • pysam >=0.11.2
  • scipy >=1.1
  • sphinx-argparse *