Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/malaria

https://github.com/broadinstitute/malaria

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 576 KB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

Malaria Plasmodium Illumina Amplicon Workspace

This workspace contains workflows for processing Plasmodium amplicon sequencing data using Illumina platforms in the Terra platform. It is panel-agnostic and includes two main workflows:

  • 01IlluminaAmplicon_Processing: Preprocesses raw reads, removes sequencing errors (denoising), and prepares data for genotyping.
  • 02PlasmodiumGenotypePopulationAnalysis: Performs genotype analysis and produces summary reports, including frequency maps of drug resistance.

Reference data and example datasets for multiple panels (e.g. MAD4HatTeR, AMPLseq, SIMPLseq) are included.

📬 Contact: publichealthgenomics@broadinstitute.org

🔗 Workspace link

🔗 Visual walkthrough link

🔗 Development guide link

Owner

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

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 18
  • Delete event: 13
  • Issue comment event: 12
  • Member event: 5
  • Push event: 78
  • Pull request event: 19
  • Create event: 9
Last Year
  • Issues event: 18
  • Delete event: 13
  • Issue comment event: 12
  • Member event: 5
  • Push event: 78
  • Pull request event: 19
  • Create event: 9

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 183
  • Total Committers: 4
  • Avg Commits per committer: 45.75
  • Development Distribution Score (DDS): 0.388
Past Year
  • Commits: 170
  • Committers: 3
  • Avg Commits per committer: 56.667
  • Development Distribution Score (DDS): 0.412
Top Committers
Name Email Commits
Jorge Romero j****1@g****m 112
brosula b****a@b****g 68
Paulo Manrique p****v@g****m 2
cmloreth 6****h 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 12
  • Total pull requests: 22
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 9 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.14
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 22
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 9 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.14
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jorgeamaya (5)
  • brosula (4)
  • dpark01 (3)
Pull Request Authors
  • jorgeamaya (13)
  • brosula (7)
  • Paulonvnv (4)
Top Labels
Issue Labels
enhancement (1) bug (1) documentation (1)
Pull Request Labels