NAME

fu-cat - Concatenate FASTA or FASTQ files

VERSION

version 1.5.8

SYNOPSIS

  fu-cat [options] [FILE1 FILE2 FILE3...]

DESCRIPTION

This program parses a list of FASTA/FASTQ and will concatenate them ensuring consistent output. Will rename duplicate sequence names. Will try to autodetect the format of all files before executing and decide accordingly the output format (FASTA if at least one of the files is FASTA, otherwise FASTQ). If reading from STDIN the first sequence is in FASTQ format, will skip all the sequences without a quality string.

If no files are provided the program will try reading from STDIN, otherwise add a '-' to the list of files to also read from STDIN.

NAME

fu-cat - concatenate FASTA or FASTQ files

PARAMETERS

-s, --separator

When a second sequence with a name that was already printed is found, the program will append a progressive number, separated by this string. Use `fu-rename` if you need more options. [default: "."]

-f, --fasta

Force FASTA output

-q, --fastq

Force FASTQ output. Will not print any sequence without quality (they will be skipped)

-d, --dereplicate

Print each sequence only only once

-5, --rename-md5

(use with -d) rename each sequence name with the MD5sum of the sequence.

-l, --minlen INT

Do not print sequences shorter (exclusive) than INT

-m, --maxlen INT

Do not print sequences longer (exclusive) than INT

-u, --uppercase

Will print the whole sequence in uppercase

-w, --width INT

Size of the FASTA lines. Specifing 0 will print the whole sequence in the same line (default: 0)

--verbose

Print more details

--help

Display this help page

--version

Print version and exit

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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