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kingfisher

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

https://github.com/wwood/kingfisher-download

Science Score: 44.0%

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
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.4%) to scientific vocabulary

Keywords

aspera-client fastq-files sra
Last synced: 7 months ago · JSON representation ·

Repository

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Basic Info
Statistics
  • Stars: 274
  • Watchers: 7
  • Forks: 42
  • Open Issues: 9
  • Releases: 3
Topics
aspera-client fastq-files sra
Created over 6 years ago · Last pushed 8 months ago
Metadata Files
Readme Citation

README.md

Welcome

Kingfisher is a fast and flexible program for procurement of sequence files (and their annotations) from public data sources, including the European Nucleotide Archive (ENA), NCBI SRA, Amazon AWS and Google Cloud. It's input is one or more "Run" accessions e.g. DRR001970, or a BioProject accessions e.g. PRJNA621514 or SRP260223.

For more documentation, see https://wwood.github.io/kingfisher-download/

Kingfisher logo

Owner

  • Name: Ben J Woodcroft
  • Login: wwood
  • Kind: user
  • Location: Brisbane, University of Queensland
  • Company: Queensland University of Technology

Informatics team leader at the Centre for Microbiome Research (CMR)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Woodcroft
    given-names: Ben J.
    orcid: https://orcid.org/0000-0003-0670-7480
  - family-names: Cunningham
    given-names: Mitchell
  - family-names: Gans
    given-names: Jason D.
  - family-names: Bolduc
    given-names: Benjamin B.
    orcid: https://orcid.org/0000-0003-2420-0755
  - family-names: Hodgkins
    given-names: Suzanne B.
    orcid: https://orcid.org/0000-0002-0489-9207
title: "Kingfisher: A utility for procurement of public sequencing data"
version: 0.4.1
date-released: 2024-01-18
doi: 10.5281/zenodo.10525085

GitHub Events

Total
  • Issues event: 2
  • Watch event: 29
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 4
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 29
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 4
  • Create event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 228
  • Total Committers: 5
  • Avg Commits per committer: 45.6
  • Development Distribution Score (DDS): 0.018
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ben Woodcroft d****n@g****m 224
Suzanne Hodgkins s****m@g****m 1
Rhys Newell 4****l 1
Josh L. Espinoza j****z@g****m 1
JamieCFreeman 3****n 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 36
  • Total pull requests: 7
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 25
  • Total pull request authors: 7
  • Average comments per issue: 3.61
  • Average comments per pull request: 1.71
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jolespin (5)
  • yuzhenpeng (2)
  • JonathonMifsud (2)
  • slbai01 (2)
  • SilasK (2)
  • Rkubinski (2)
  • AroneyS (2)
  • mbhall88 (1)
  • shandas29 (1)
  • FionaMoon (1)
  • Guanxin1996 (1)
  • ShailNair (1)
  • jknp (1)
  • AssumeAssume (1)
  • 1onic (1)
Pull Request Authors
  • linsalrob (2)
  • ATpoint (1)
  • MakeTheBrainHappy (1)
  • rhysnewell (1)
  • jolespin (1)
  • JamieCFreeman (1)
  • shodgkins (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 74 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 2
pypi.org: kingfisher

Download/extract biological FASTA/Q read data and metadata

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 74 Last month
Rankings
Stargazers count: 4.7%
Forks count: 6.8%
Dependent packages count: 10.1%
Average: 13.0%
Dependent repos count: 21.6%
Downloads: 22.0%
Maintainers (2)
wwood AroneyS
Last synced: 7 months ago

Dependencies

setup.py pypi
  • bird_tool_utils_python *
  • extern *
  • pandas *
  • pyarrow *
  • requests *
  • tqdm *
.github/workflows/deploy-docs.yml actions
  • actions-rs/toolchain v1.0.6 composite
  • actions/checkout v3 composite
  • crazy-max/ghaction-github-pages v3.0.0 composite
.github/workflows/publish-to-pypi.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • casperdcl/deploy-pypi v2 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite