NAME

fu-cat - concatenate FASTA or FASTQ files

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.

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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