Snakebite-GBS

The snakemake pipeline based on GBS-SNP-Crop and further extended.

Overview

A functional, simplified workflow of the pipeline

DAG

The visual overview of the various rules of the pipeline

Configuration

The pipeline parameter configuration takes place in the file

Snakebite-GBS_config.yaml

Further, the settings important for the computing cluster are defined here:

Snakebite-GBS_server-config.yaml

Starting the pipeline

Currently, the default configuration is such that the pipelines makes use of docker/singularity. If you plan to use local software installation and or conda environments, you would need to install the required tools manually.

Once the environment is created, you are ready to go.

To start the pipeline, just type

bash run_Snakebite-GBS.sh

You can initiate a dry-run by running

bash run_Snakebite-GBS.sh -np

More information

For further information, please visit the wiki page here: https://github.com/fischuu/Snakebite-GBS/wiki

Current state

The pipeline is currently under active development, unstable development versions with the latest features can be found in the dev branch (odd version numbers), the main branch should be the latest stable version (even version numbers).

Possible use-cases

Complete de-novo approach

No previous information available, just a set of FASTQ-files as input

Reference genome available

Here, we have the FASTQ files and an existing reference genome in FASTA format

Mock reference anmd variant set available

Here, we ran a previous de-novo approach and obtained from there a set of variants in VCF format and also a mock reference in fasta format

Reference genome and variant set available

A reference genome as well as a set of variants is available.

FUNDING

The development of this pipeline received funding from the ARCTAQUA project (https://site.nord.no/arctaqua/) and GENOTYPE, Natural Resources Institute Finland (LUKE) (https://www.luke.fi)