NAME

fu-uniq - Dereplicate sequences

VERSION

version 1.5.8

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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) 2018-2023 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License