https://github.com/telatin/seqfu2
:rocket: seqfu - Sequece Fastx Utilities
https://github.com/telatin/seqfu2
bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing
Last synced: 6 months ago
JSON representation
:rocket: seqfu - Sequece Fastx Utilities
- Host: GitHub
- URL: https://github.com/telatin/seqfu2
- Owner: telatin
- License: gpl-3.0
- Created: 2020-11-26T15:50:15.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2025-10-07T11:08:36.000Z (7 months ago)
- Last Synced: 2025-10-07T11:35:52.354Z (7 months ago)
- Topics: bioconda, bioinformatics, bioinformatics-tool, fasta, fastq, genomics, ngs, sequencing
- Language: Nim
- Homepage: https://telatin.github.io/seqfu2
- Size: 78.2 MB
- Stars: 120
- Watchers: 3
- Forks: 9
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
- Awesome-Bioinformatics - SeqFu - Sequence manipulation toolkit for FASTA/FASTQ files written in Nim. [ [paper-2021](https://www.mdpi.com/2306-5354/8/5/59) | [web](https://telatin.github.io/seqfu2/) ] (Next Generation Sequencing / Sequence Processing)
README
# SeqFu
[](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml)
[](https://bioconda.github.io/recipes/seqfu/README.html)
[](https://github.com/telatin/seqfu2/releases)
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](https://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**](https://telatin.github.io/seqfu2)
## Splash screen
