NAME

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

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.

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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