Home

How To : Running Grandeur

Grandeur is a nextflow workflow for working with bacterial isolates in a public health setting.

Quickstart

See USAGE for more information and Examples for examples.

nextflow run UPHL-BioNGS/Grandeur -profile docker --reads /path/to/reads/directory --fastas /path/to/fastas/directory 

The Problem

All "good" bioinformatic tools and workflows are trying to solve a problem. At UPHL, we ran into a problem that there was not a workflow that met our sequencing analysis needs for bacterial isolates.

We needed a bioinformatic workflow to replace the bench experiments for

• E. coli O and H characterization
• Shigella CadA and IpaH characterization
• Vibrio speciation
• Salmonella serotyping

We also needed something to assist our local epidemiologists in outbreak investigations

• Species agnostic core genome alignment and phylogenetic trees
• SNP matrices
• AMR gene identification

Grandeur is species-agnostic at its core, although certain organisms undergo some species-specific processes. Future directions include speciation of unknown isolates. Our initial testing seemed promising, but we have not tested this use enough to make it widely available.

Grandeur includes a de novo assembly workflow, but can also run on contig/fasta files generated from other workflows. Our most common files are those generated from PHOENIX, CDC's ARLN workflow, and DONUT FALLS, a UPHL-generated nanopore sequencing workflow.

More information about using Grandeur and what its subworkflows do can be found in this Wiki.

If you are running into bugs or other issues, please post in the issues tracker.