/ 
Proch-N50-1.7.0
River stage zero No dependents
/ fu-sort

NAME

fu-sort - Sort sequences by size

VERSION

version 1.7.0

SYNOPSIS

fu-sort [options] filename [...]

DESCRIPTION

fu-sort reads FASTA/FASTQ files and sorts sequences by length in either ascending or descending order. It provides various output formatting options and can handle both FASTA and FASTQ formats.

NAME

fu-sort - Sort sequences by size with flexible output formatting

OPTIONS

Sorting Options

--asc

Sort sequences in ascending order (default: descending)

Output Formatting

--w, --line-width N

Width for FASTA sequence lines (0 for unlimited)

--sc, --strip-comments

Remove sequence comments

--fasta

Force FASTA output format

--fastq

Force FASTQ output format

--rc

Output reverse complement sequences

--q, --qual n.n

Default quality score for FASTQ output

--u, --upper

Convert sequences to uppercase

Sequence Annotation

--al, --add-length

Add sequence length to comments

Other Options

--quiet

Suppress progress messages

--debug

Enable debug output

--version

Display version information

--help

Show this help message

EXAMPLES

Sort sequences by length (longest first):

fu-sort input.fa > sorted.fa

Sort sequences by length (shortest first):

fu-sort --asc input.fa > sorted.fa

Sort and add length information:

fu-sort --add-length input.fa > sorted_with_length.fa

Convert to FASTA with wrapped sequences:

fu-sort --fasta --line-width 60 input.fastq > wrapped.fa

MODERN ALTERNATIVE

This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis. This suite is maintained for the higher portability of Perl scripts under certain circumstances.

SeqFu is available at https://github.com/telatin/seqfu2, and can be installed with BioConda conda install -c bioconda seqfu

CITING

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018-2027 by Quadram Institute Bioscience.

This is free software, licensed under:

The MIT (X11) License