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seqfu

:rocket: seqfu - Sequece Fastx Utilities

https://github.com/telatin/seqfu2

Science Score: 49.0%

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 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: mdpi.com
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary

Keywords

bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing
Last synced: 6 months ago · JSON representation

Repository

:rocket: seqfu - Sequece Fastx Utilities

Basic Info
Statistics
  • Stars: 114
  • Watchers: 3
  • Forks: 9
  • Open Issues: 0
  • Releases: 61
Topics
bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing
Created about 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

SeqFu

Seqfu-Nim-Build Last Commit Downloads Latest release

A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths.

📦 Installation

Seqfu can be easily installed via Miniconda:

bash conda install -y -c conda-forge -c bioconda "seqfu>1.10"

Build from source

Building the Nim programs alone would just require a nimble build, but this would leave out some other utilities. There is a make (Makefile) building system. Since Nim is not so popular, I describe a full installation:

```bash

Do you have building tools? You will need C and make, in Ubuntu:

sudo apt install build-essential

Install zlib

sudo apt install zlib1g-dev

Install Nim 2.0

curl https://nim-lang.org/choosenim/init.sh -sSf | sh

Clone this repo

git clone https://github.com/telatin/seqfu2

Compile and test

cd seqfu2 make make test

All binaries are in bin (move them in a location in your $PATH)

```

📰 Citation

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059

bibtex @article{seqfu, title = {SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files}, author = {Telatin, Andrea and Fariselli, Piero and Birolo, Giovanni}, year = 2021, journal = {Bioengineering}, volume = 8, number = 5, doi = {10.3390/bioengineering8050059}, issn = {2306-5354}, url = {https://www.mdpi.com/2306-5354/8/5/59}, article-number = 59, pubmedid = 34066939 }

📙 Full documentation

The full documentation is available at: telatin.github.io/seqfu2

Splash screen

`seqfu`

Owner

  • Name: Andrea Telatin
  • Login: telatin
  • Kind: user
  • Location: Norwich, UK
  • Company: Quadram Institute Bioscience

Bioinformatician @quadram-institute-bioscience

GitHub Events

Total
  • Create event: 3
  • Issues event: 3
  • Release event: 1
  • Watch event: 9
  • Issue comment event: 3
  • Push event: 3
  • Fork event: 2
Last Year
  • Create event: 3
  • Issues event: 3
  • Release event: 1
  • Watch event: 9
  • Issue comment event: 3
  • Push event: 3
  • Fork event: 2

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 20
  • Total pull requests: 8
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 16 hours
  • Total issue authors: 13
  • Total pull request authors: 7
  • Average comments per issue: 1.85
  • Average comments per pull request: 0.25
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 4
  • Pull requests: 3
  • Average time to close issues: 5 days
  • Average time to close pull requests: 1 day
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 2.75
  • Average comments per pull request: 0.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • telatin (8)
  • tamuanand (1)
  • JeanMainguy (1)
  • iamh2o (1)
  • michaelgelliot (1)
  • nolanmaier (1)
  • SciLiciumTheo (1)
  • pontushojer (1)
  • simone-pignotti (1)
  • dialvarezs (1)
  • kabilov (1)
  • ImagoXV (1)
  • RachBioHaz (1)
  • jdidion (1)
Pull Request Authors
  • thanhleviet (2)
  • dialvarezs (2)
  • martin-g (2)
  • microbiomes (2)
  • github-actions[bot] (1)
  • codacy-badger (1)
  • telatin (1)
Top Labels
Issue Labels
bug (3) feature request (2) enhancement (1) seqfu 0.x (1) seqfu_2.x (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 71
proxy.golang.org: github.com/telatin/seqfu2
  • Versions: 69
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 6 months ago
spack.io: seqfu

seqfu - Sequece Fastx Utilities

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Average: 29.2%
Dependent packages count: 58.4%
Last synced: 6 months ago

Dependencies

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Dockerfile docker
  • debian stretch-slim build
scripts/.docker/Dockerfile docker
  • ubuntu 14.04 build