Lougheed Lab GTseq Pipeline

WORK IN PROGRESS.

GTseq pipeline derived from work done by Peiwen Li, Kristen Hayward, and others, with portions inspired by the GTseq pipeline by Nate Campbell.

System Requirements

This software must be run on a machine running Linux.

Installation

1. Install/load bcl2fastq2 if needed.
2. Install/load bcftools if needed.
3. Install the Lougheed Lab GTseq pipeline via pip: pip install lougheed_gtseq
4. TODO

Usage

1. Prepare a sample sheet

It should have the following headers: Sample_name, Plate_ID, i7_name, i5_name.

There must be exactly one entry for a sample; additional replicates should have a unique suffix (e.g., -1, -2) added to the end of the sample name.

2. TODO

TODO

Copyright Notice

Lougheed Lab GTseq pipeline.
Copyright (C) 2024 David Lougheed

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 https://www.gnu.org/licenses/.