https://github.com/biojulia/fastx.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.

Science Score: 46.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
1 of 13 committers (7.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary

Keywords

bio biojulia fasta fasta-files fasta-format fastq fastq-files fastq-format file-format julia parsing

Keywords from Contributors

biology biological-sequences bioinformatics numerical programming-language julialang data-frame dataframes tabular-data microbiome

Last synced: 5 months ago · JSON representation

Repository

Parse and process FASTA and FASTQ formatted files of biological sequences.

Basic Info

Host: GitHub
Owner: BioJulia
License: mit
Language: Julia
Default Branch: master
Homepage: https://biojulia.dev
Size: 1.09 MB

Statistics

Stars: 65
Watchers: 8
Forks: 20
Open Issues: 6
Releases: 16

Topics

bio biojulia fasta fasta-files fasta-format fastq fastq-files fastq-format file-format julia parsing

Created over 7 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Funding License

README.md

FASTX

Description

FASTX provides I/O and utilities for manipulating FASTA and FASTQ, formatted sequence data files.

Installation

You can install FASTX from the julia REPL. Press ] to enter pkg mode, and enter the following:

julia add FASTX

If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.

Testing

FASTX is tested against Julia 1.X on Linux, OS X, and Windows.

Latest build status:

Contributing

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.

Backers & Sponsors

Thank you to all our backers and sponsors!

Questions?

If you have a question about contributing or using BioJulia software, come on over and chat to us on the Julia Slack workspace, or you can try the Bio category of the Julia discourse site.

Owner

Name: BioJulia
Login: BioJulia
Kind: organization

Website: https://biojulia.dev
Repositories: 79
Profile: https://github.com/BioJulia

Bioinformatics and Computational Biology in Julia

GitHub Events

Total

Issues event: 2
Watch event: 4
Issue comment event: 3
Push event: 6
Pull request event: 8
Fork event: 1

Last Year

Issues event: 2
Watch event: 4
Issue comment event: 3
Push event: 6
Pull request event: 8
Fork event: 1

Committers

Last synced: 8 months ago

All Time

Total Commits: 114
Total Committers: 13
Avg Commits per committer: 8.769
Development Distribution Score (DDS): 0.526

Past Year

Commits: 10
Committers: 1
Avg Commits per committer: 10.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Jakob Nybo Nissen	j**n@g**m	54
Ben J. Ward	b**d@p**m	23
Ben J. Ward	w**0@g**m	20
Nicholas Bauer	n**r@o**m	4
Kevin Bonham	k**m@g**m	2
Harry Scholes	h****s	2
Ciarán O'Mara	C**a@u**u	2
Kevin Bonham	k**n@b**h	2
github-actions[bot]	4****]	1
dehann	d****n	1
Tim Holy	t**y@g**m	1
Thomas Poulsen	t**s@l**k	1
blaiseli	b**b@n**g	1

Committer Domains (Top 20 + Academic)

nsup.org: 1 lha66.dk: 1 bonham.ch: 1 utas.edu.au: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 48
Total pull requests: 80
Average time to close issues: 4 months
Average time to close pull requests: about 1 month
Total issue authors: 26
Total pull request authors: 12
Average comments per issue: 4.67
Average comments per pull request: 1.58
Merged pull requests: 67
Bot issues: 0
Bot pull requests: 4

Past Year

Issues: 1
Pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: about 1 hour
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 1.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jakobnissen (16)
SabrinaJaye (5)
jtackm (2)
blaiseli (2)
jonathanBieler (2)
anton083 (1)
tp2750 (1)
JuliaTagBot (1)
godkin1211 (1)
pfarndt (1)
kescobo (1)
mmattocks (1)
reganbaucke (1)
fethalen (1)
cecileane (1)

Pull Request Authors

jakobnissen (62)
github-actions[bot] (5)
SabrinaJaye (5)
kescobo (3)
BioTurboNick (2)
harryscholes (2)
dehann (1)
motorny (1)
CiaranOMara (1)
tp2750 (1)
blaiseli (1)

Top Labels

Issue Labels

enhancement (1) wontfix (1)

Pull Request Labels

do not squash (1)

Packages

Total packages: 1
Total downloads:
- julia 615 total

Total dependent packages: 19
Total dependent repositories: 0
Total versions: 17

juliahub.com: FASTX

Parse and process FASTA and FASTQ formatted files of biological sequences.

Homepage: https://biojulia.dev
Documentation: https://docs.juliahub.com/General/FASTX/stable/
License: MIT
Latest release: 2.1.7
published over 1 year ago

Versions: 17
Dependent Packages: 19
Dependent Repositories: 0
Downloads: 615 Total

Rankings

Dependent packages count: 4.1%

Average: 9.6%

Forks count: 9.8%

Dependent repos count: 9.9%

Stargazers count: 14.3%

Last synced: 6 months ago

Dependencies

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julia-actions/setup-julia latest composite

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