Conda recipes for the bioconda channel.

🆔 Scan contig files against PubMLST typing schemes

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

BEAV: Bacterial Element Annotation reVamped

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

🧬 Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers

An in silico tool to predict Shigella serotypes

Oxford Nanopore Technologies (ONT) long-read assembly polishing tool

The fun things we use and share at UPHL

Containerized version of QuAISAR

Rapid identification of bacterial species from FASTA contigs

Various pipelines and scripts used by the CO state public health lab