README.md

SeqFu

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.

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📦 Installation

Seqfu can be easily installed via Miniconda:

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:

# 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

@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

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