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This is the home of SeqFu, where 2.0 is under development. The stable SeqFu 1.x has been moved to a new home (seqfu_v1). |
# SeqFu
[](https://github.com/telatin/seqfu2/actions/workflows/make.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
