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🚀 seqfu - Sequece Fastx Utilities
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telatin/seqfu2
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A general-purpose program to manipulate and parse information from FASTA/FASTQ files,supporting gzipped input files.Includes functions tointerleave andde-interleave FASTQ files, torenamesequences and tocount and printstatistics on sequence lengths.
Seqfu can be easily installed via Miniconda:
conda install -y -c conda-forge -c bioconda"seqfu>1.10"Building the Nim programs alone would just require animble build,but this would leave out some other utilities.There is amake (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 zlibsudo apt install zlib1g-dev# Install Nim 2.0curl https://nim-lang.org/choosenim/init.sh -sSf| sh# Clone this repogit clone https://github.com/telatin/seqfu2# Compile and testcd seqfu2makemaketest# All binaries are in bin (move them in a location in your $PATH)
Telatin A, Fariselli P, Birolo G.SeqFu: A Suite of Utilities for the Robustand 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}
The full documentation is available at:telatin.github.io/seqfu2
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🚀 seqfu - Sequece Fastx Utilities