Dataset Information

Sequanix: a dynamic graphical interface for Snakemake workflows.

ABSTRACT: Summary:We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users. Availability and implementation:Source on http://github.com/sequana/sequana, bio-containers on http://bioconda.github.io and Singularity hub (http://singularity-hub.org). Contact:dimitri.desvillechabrol@pasteur.fr or thomas.cokelaer@pasteur.fr. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Desvillechabrol D

PROVIDER: S-EPMC5972652 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Sequanix: a dynamic graphical interface for Snakemake workflows.

Desvillechabrol Dimitri D Legendre Rachel R Rioualen Claire C Bouchier Christiane C van Helden Jacques J Kennedy Sean S Cokelaer Thomas T

Bioinformatics (Oxford, England) 20180601 11

<h4>Summary</h4>We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to bo ...[more]

PMID: 29361152

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Project description:BackgroundIn the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise.ResultsHere we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license.ConclusionsHISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses.

Dataset Information

Sequanix: a dynamic graphical interface for Snakemake workflows.

Publications

Sequanix: a dynamic graphical interface for Snakemake workflows.

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