lmc297

BTyper3

In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

bactaxR

Bacterial taxonomy construction and evaluation in R

seq2mlst

In silico multi-locus sequence typing (MLST) for bacterial genomes

BTyper

Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

SNPBac

SNP and variant calling pipeline for bacteria

besPLOT

Interactive PCA and NMDS plots

2017_AEM_Figure_S2

Interactive plots of NMDS results

BMiner

A companion application for analyzing and viewing BTyper output files in aggregate

bgc_workshop

Materials for the BGC detection workshop

bioconda-recipes

Conda recipes for the bioconda channel.

BRisk

Bacillus cereus exposure/evaluation of risk (beta)

fsl_wgs_pipeline

Whole-genome sequencing quality control and assembly pipeline

Group_III_bacillus_cereus

Supplementary material for the 2019-2020 cereulide-producing Group III B. cereus s.l. phylogenomics study

homebrew-btyper

homebrew-btyper-testing

homebrew-btyper3

Homebrew formula for BTyper3

homebrew-core

🍻 Default formulae for the missing package manager for macOS

homebrew-seq2mlst

Tap for seq2mlst (in silico MLST tool)

homebrew-snpbac

jfp_sublethal_heat_stress_modeling

Statistical analyses conducted for Journal of Food Protection sublethal heat stress modeling paper

LRNRisk

Materials for the LRNRisk project

NYS_Typhimurium_2018

Supplementary material for the 2018 New York state Typhimurium project

rna_seq_workshop_uzh_2017

Materials for the RNA-Seq Data Analysis Workshop at the University of Zurich, February 16, 2017

rna_seq_workshop_uzh_2018

Materials for the RNA-Seq Data Analysis Workshop at the University of Zurich, April 6, 2018

ScriptCity

Random (meta)genomics/(meta)transcriptomics-related scripts

skylinetools

Utilities and distributions for (birth-death) skyline models.

ubc_wgs_workshop_2019

Materials for the bacterial whole-genome sequencing data analysis workshop at the University of British Columbia, April-May 2019

zru_farms

Supplementary data for the ZRU Farms Salmonella project