NAME

fu-uniq - Dereplicate sequences

VERSION

version 1.5.0

SYNOPSIS

fu-uniq [options] input.fa > uniq.fa

PARAMETERS

• --k|keepname

  Use first sequence name as cluster name(default ON)

• --p|prefix [X]

  Sequence prefix (default 'seq')

• --s|separator [X]

  Prefix and counter separator (default '.')

• --m|min-size [N]

  Print only sequences found at least N times (default '0')

• --size-as-comment

  Add size as comment, not as part of sequence name (default OFF)

General

• --help

  This help

• --version

  Print version and exit

• --citation

  Print citation for seqfu

• --quiet

  No screen output (default OFF)

• --debug

  Debug mode: keep all temporary files (default OFF)

Common seqfu options

• --w|line-width [N]

  FASTA line size (0 for unlimited) (default '80')

• --strip

  Strip comments

• --fasta

  Force FASTA output

• --fastq

  Force FASTQ output

• --rc

  Print reverse complementary

• --q|qual [n.n]

  Default quality for FASTQ files (default '32')

• --upper

  Convert sequence to uppercase

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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) 2018-2022 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License