Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/isham_wgs

ISHAM fungal whole genome sequencing benchmark project

https://github.com/broadinstitute/isham_wgs

Science Score: 57.0%

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
  • ✓
    Institutional organization owner
    Organization broadinstitute has institutional domain (www.broadinstitute.org)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords from Contributors

transformation
Last synced: 7 months ago · JSON representation

Repository

ISHAM fungal whole genome sequencing benchmark project

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 61.8 MB
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme

README.md

ISHAM Fungal WGS protocol benchmarking

Comparison of genomic variant identification protocols for Candidas auris

Background

This is a consortium effort from the International Society for Human and Animal Mycology (ISHAM) community, with 11 independent groups across four continents, for the aim of establishing a best practice of genomic variant identification pipeline. For convenors and members of the working group, check below.

Repository

This is a repository with data and analysis script needed to reproduce most of the analyses benchmarking genomic variant identification protocols for the fungal community.

The repository was structured as follows: - data: data needed - figs: figures reproduced from the jupyter notebook. - analysis.ipynb: jupyter notebook to reproduce results from the corresponding manuscript. - README.md: this file.

Usage & Dependencies

To reproduce figures from the manuscript, make sure the following tools are available - Python >= 3.4 - pip3 >=20.1.1

Install the following python 3 packages via pip: sh pip install statistics matplotlib pandas numpy funpipe=0.1.0 jupyter

Clone this repo: sh git clone git://github.com/broadinstitute/isham_wgs.git cd isham_wgs jupyter notebook analysis.ipynb Note that additional tools and the raw VCF files are needed to reproduce the analysis from scratch, including: - vcftools-v0.1.15 - zlib-1.2.11 - bcftools-v1.8 - htslib-v1.10.2 (bgzip and tabix)

Uncomment bash sections of the notebook to fully reproduce the analysis.

Data Availability

All raw data's submitted to NCBI. Important outputs are shared in this figshare project. Check here for paths to the submitted files from all 12 groups.

Working group: Genomic Epidemiology of Fungal Infections

Overview, Achievements and Publications

Convenor(s) * Christina Cuomo (cuomo@broadinstitute.org) * Anastasia Litvintseva (frq8@cdc.gov) * Ana Alastruey-Izquierdo (anaalastruey@isciii.es) * Matthew Fisher (matthew.fisher@imperial.ac.uk) * David Engelthaler (dengelthaler@tgen.org)

Citation

To citate this work, use the following:

Li X, Muñoz JF, Gade L, Argimon S, Bougnoux ME, Bowers JR, Chow NA, Cuesta I, Farrer RA, Maufrais C, Monroy-Nieto J, Pradhan D, Uehling J, Vu D, Yeats CA, Aanensen DM, d'Enfert C, Engelthaler DM, Eyre DW, Fisher MC, Hagen F, Meyer W, Singh G, Alastruey-Izquierdo A, Litvintseva AP, Cuomo CA. Comparing genomic variant identification protocols for Candida auris. Microb Genom. 2023 Apr;9(4). doi: 10.1099/mgen.0.000979. PMID: 37043380.

Issues

Contact Xiao Li (xiaoli@broadinstitute.org) if you have any analysis related questions. Submit an issue for bugs.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 13
  • Total Committers: 3
  • Avg Commits per committer: 4.333
  • Development Distribution Score (DDS): 0.154
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
xiaolicbs x****s@g****m 11
jofmunoz 3****z 1
xiaoli0 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total 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
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
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels