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SeqFu

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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.


Installation

Seqfu can be easily installed via Miniconda:

conda install -y -c bioconda seqfu

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

Full documentation

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

Splash screen

SeqFu - Sequence Fastx Utilities
version: 1.0.0

        • count [cnt]         : count FASTA/FASTQ reads, pair-end aware
        • deinterleave [dei]  : deinterleave FASTQ
        • derep [der]         : feature-rich dereplication of FASTA/FASTQ files
        • interleave [ilv]    : interleave FASTQ pair ends
        • lanes [mrl]         : merge Illumina lanes
        • sort [srt]          : sort sequences by size (uniques)
        • stats [st]          : statistics on sequence lengths

        • cat                 : concatenate FASTA/FASTQ files
        • grep                : select sequences with patterns
        • head                : print first sequences
        • rc                  : reverse complement strings or files
        • tail                : view last sequences
        • view                : view sequences with colored quality and oligo matches

Add --help after each command to print usage