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