NAME

make_metadata.pl - a script to draft a metadata table for Qiime 2 or Lotus.

The program will ensure that the proper number of files (1 or 2) is found for each sample, and that the sample ID (initial part of the filename) does not contain unsupported chars.

AUTHOR

Andrea Telatin <andrea.telatin@quadram.ac.uk>

SYNOPSIS

make_metadata.pl [options] -i INPUT_DIR

PARAMETERS

-i, --reads DIR

Path to the directory containing the FASTQ files

-s, --single-end

Input directory contains unpaired files (default is Paired-End mode)

-1, --for-tag STRING

Tag to detect that a file is forward (default: _R1)

-2, --rev-tag STRING

Tag to detect that a file is forward (default: _R2)

-d, --delim STRING

The sample ID is the filename up to the delimiter (default: _)

-a, --abs-path

Include the absolute path to the metadata file

-l, --lotus

Print metadata in LOTUS format (default)

-q, --qiime

Print metadata in Qiime2 format (default: Lotus)

-b, --barcode

Add a placeholder for the barcode (default: NNNNNNNN, use -r for a random unique barcode)

-r, --random-bc

When adding a barcode (see -b), will generate a random unique sequence instead of NNNNNNNN

BUGS

Please report them to <andrea@telatin.com>

COPYRIGHT

Copyright (C) 2013-2020 Andrea Telatin

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.