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Welcome to the Grandeur wiki!

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.

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