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binning-refiner

Improving genome bins through the combination of different binning programs

https://github.com/songweizhi/binning_refiner

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary

Keywords

binning binning-refiner bioinformatics metagenomics refinement
Last synced: 6 months ago · JSON representation

Repository

Improving genome bins through the combination of different binning programs

Basic Info
  • Host: GitHub
  • Owner: songweizhi
  • License: agpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 87.6 MB
Statistics
  • Stars: 31
  • Watchers: 5
  • Forks: 4
  • Open Issues: 1
  • Releases: 0
Topics
binning binning-refiner bioinformatics metagenomics refinement
Created over 9 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.md

logo

pypi licence pypi version pypi download DOI

Publication

  • Song WZ, Thomas T (2017) Binning_refiner: Improving genome bins through the combination of different binning programs. Bioinformatics, 33(12), 1873-1875. PDF
  • Weizhi Song (songwz03@gmail.com), Torsten Thomas(t.thomas@unsw.edu.au)
  • The Centre for Marine Bio-Innovation (CMB), University of New South Wales, Sydney, Australia

Dependencies:

Change Log:

Version 1.4.0 (2019-04-19): + Binning_refiner can now supports MORE THAN THREE binning programs.

Version 1.3 (2019-01-06): + Binningrefiner can now be installed with "pip install Binningrefiner".

Version 1.2 (2017-11-30): + Binning_refiner has been simplified to keep only the core functions, which made it much easier to install and use, hope you enjoy it :)

Important message

  1. Binning_refiner can now supports MORE THAN THREE binning programs.

  2. Binningrefiner can now be installed with "pip install Binningrefiner".

  3. An independent R version of Binningrefiner is available now [Binning_refiner.R]. The R packages seqinr, assertr, tidyr, tools, optparse, googleVis are required for running Binningrefiner.R.

  4. In the original version of Binningrefiner, the blast approach (as described in its publication) was used to identify the same contig among input bin sets. As Binningrefiner was designed to refine bins derived from the same set of assemblies and the blast step is time-consuming (especially for big dataset), the same assembly among different bin sets was identified by its ID rather than blastn, which made Binning_refiner much faster to run and more easier to install.

How to install:

  • Binning_refiner can be installed with pip now:

    # For installation
pip install Binning_refiner

# For update
pip install --upgrade Binning_refiner

  • Visualisation of the correlations between input bins (figure below) can be enabled with '-plot' option. The R packages optparse and googleVis are needed for this function.

Help information:

    Binning_refiner -h

      -i          input bin folder
      -p          output prefix
      -m          minimal size (Kbp) of refined bin, default: 512
      -plot       visualize refinement with Sankey plot
      -x          the width of sankey plot
      -y          the height of sankey plot
      -q          silent progress report

How to run:

  1. The input for Binning_refiner v1.4 is a folder hold all input bins derived from the same set of assemblies, with each binning program produced bins stored in a separated sub-folder. Here is an example of the inputbinfolder.

  2. All bin files in the same sub-folder must have the same extension.

  3. Binning_refiner now compatible with both python2 and python3.

    # example command
Binning_refiner -i input_bin_folder -p Human -plot

# For R version Binning_refiner
Rscript path/to/Binning_refiner.R -i input_bin_folder -p Human

Output files:

  1. All refined bins larger than defined bin size cutoff.

  2. The id of the contigs in each refined bin.

  3. The size of refined bins and where its contigs come from.

  4. Visualisation of binning refinement.

    Sankey_plot

Owner

  • Name: Weizhi Song
  • Login: songweizhi
  • Kind: user
  • Location: Hong Kong
  • Company: The Chinese University of Hong Kong

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 177
  • Total Committers: 4
  • Avg Commits per committer: 44.25
  • Development Distribution Score (DDS): 0.034
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
songweizhi s****3@g****m 171
Ben Woodcroft d****n@g****m 3
Weizhi SONG w****g@s****u 2
songweizhi s****i@p****u 1
Committer Domains (Top 20 + Academic)
pro-song.ad.unsw.edu.au: 1 student.unsw.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 2
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: about 8 hours
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 1.67
  • Average comments per pull request: 1.5
  • Merged pull requests: 1
  • 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
  • palomo11 (1)
  • mewu3 (1)
  • keuv-grvl (1)
Pull Request Authors
  • wwood (1)
  • lobrien20 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 31 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: binning-refiner

Binning_refiner

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 31 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 11.5%
Forks count: 15.3%
Average: 20.6%
Dependent repos count: 21.7%
Downloads: 44.5%
Maintainers (1)
songweizhi
Last synced: 6 months ago

Dependencies

Binning_refiner.egg-info/requires.txt pypi
  • biopython *