NAME

fqlen.pl - A demo implementation to filter fastx files by length

VERSION

version 1.5.1

SYNOPSIS

fqc [options] [FILE1 FILE2 FILE3...]

DESCRIPTION

This program parses a list of FASTA/FASTQ files printing the number of sequences found in each file. Reads both uncompressed and GZipped files. Default output is the filename, tab, sequence count. Can be changed with options.

The table "key" is the absolute path of each input file, but the printed name can be changed with options.

PARAMETERS

FILE NAME

-a, --abspath

Print the absolute path of the filename (the absolute path is always the table key, but if relative paths are supplied, they will be printed).

-m, --min INT

Minimum length to print a sequence

-x, --max INT

Maximum length to print a sequence

-l, --len

Add read length as comment

-f, --fasta

Force FASTA output (default: as INPUT)

-w, --fasta-width INT

Paginate FASTA sequences (default: no)

-n, --namescheme

Sequence name scheme:

-p, --prefix STR

Use as sequence name prefix this string

-c, --strip-comment

Remove sequence comment (default: no)

--verbose

Add verbose feedback on % of printed reads

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2019 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License