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ragtag

Tools for fast and flexible genome assembly scaffolding and improvement

https://github.com/malonge/ragtag

Science Score: 46.0%

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
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords

gap-filling genome-assembly scaffolding
Last synced: 7 months ago · JSON representation

Repository

Tools for fast and flexible genome assembly scaffolding and improvement

Basic Info
  • Host: GitHub
  • Owner: malonge
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 278 KB
Statistics
  • Stars: 527
  • Watchers: 8
  • Forks: 52
  • Open Issues: 85
  • Releases: 8
Topics
gap-filling genome-assembly scaffolding
Created about 6 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

logo_text

RagTag

DOI RELEASE CONDA GitHub

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

RagTag also provides command line utilities for working with common genome assembly file formats.

logo_text

Getting Started

```bash

install with conda

conda install -c bioconda ragtag

correct a query assembly

ragtag.py correct ref.fasta query.fasta

scaffold a query assembly

ragtag.py scaffold ref.fasta query.fasta

scaffold with multiple references/maps

ragtag.py scaffold -o out1 ref1.fasta query.fasta ragtag.py scaffold -o out2 ref2.fasta query.fasta ragtag.py merge query.fasta out_/.agp other.map.agp

use Hi-C to resolve conflicts

ragtag.py merge -b hic.bam query.fasta out_/.agp other.map.agp

make joins and fill gaps in target.fa using sequences from query.fa

ragtag.py patch target.fa query.fa ```

Docs

Please see the Wiki for detailed documentation.

Dependencies

  • Minimap2, Unimap, or Nucmer
  • Python 3 (with the following auto-installed packages)
    • numpy
    • intervaltree
    • pysam
    • networkx

Citation

RagTag supersedes RaGOO:

Acknowledgments

Many of the major algorithmic improvements relative to RaGOO's first release were provided by Aleksey Zimin, lead developer of the MaSuRCA assembler. Luca Venturini suggested and initially implemented many feature enhancements, such as pysam integration. RagTag "merge" was inspired by CAMSA. The developer of CAMSA, Sergey Aganezov, helped review relevant RagTag code. RagTag "patch" was inspired by Grafter, a scaffolding tool written by Melanie Kirsche. Melanie provided guidance for the RagTag implementation. Michael Schatz has provided guidance for the whole project.

Owner

  • Name: Michael Alonge
  • Login: malonge
  • Kind: user

Computational Biologist at Ohalo Genetics

GitHub Events

Total
  • Issues event: 13
  • Watch event: 39
  • Issue comment event: 10
  • Fork event: 3
Last Year
  • Issues event: 13
  • Watch event: 39
  • Issue comment event: 10
  • Fork event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 251
  • Total Committers: 2
  • Avg Commits per committer: 125.5
  • Development Distribution Score (DDS): 0.004
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
malonge m****1@g****m 250
Alex Leonard a****d@u****h 1
Committer Domains (Top 20 + Academic)
usys.ethz.ch: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 138
  • Total pull requests: 4
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 123
  • Total pull request authors: 2
  • Average comments per issue: 2.09
  • Average comments per pull request: 0.5
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 0
  • Average time to close issues: about 13 hours
  • Average time to close pull requests: N/A
  • Issue authors: 12
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zhousun21 (4)
  • mrvollger (2)
  • nickgladman (2)
  • mictadlo (2)
  • eddykay310 (2)
  • evoecogen-git (2)
  • yuzhenpeng (2)
  • CAShuangchao (2)
  • taprs (2)
  • horvathdp (2)
  • zanfona734 (2)
  • mabh5 (2)
  • Yutang-ETH (2)
  • rahulnutron (1)
  • akhtarmzn2010 (1)
Pull Request Authors
  • twrightsman (2)
  • Neato-Nick (2)
Top Labels
Issue Labels
enhancement (3) bug (3) question (3) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 116 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 8
  • Total maintainers: 1
pypi.org: ragtag

Fast reference-guided genome assembly scaffolding

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 116 Last month
Rankings
Stargazers count: 3.3%
Forks count: 6.4%
Average: 10.0%
Dependent packages count: 10.0%
Dependent repos count: 11.6%
Downloads: 18.4%
Maintainers (1)
malonge
Last synced: 8 months ago

Dependencies

setup.py pypi
  • intervaltree *
  • networkx *
  • numpy *
  • pysam *