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adaptive

bacmet

Abricate compatible DNA based queries for bactmet database http://bacmet.biomedicine.gu.se/

bio_hansel_benchmarking

This repository is for scripts used to produce or analyze data for the bio_hansel manuscript

bioconda-recipes

Conda recipes for the bioconda channel.

bip

Bacterial Identification Pipeline

cansnp

Prototyping cannonical SNP scheme development

chewbbaca

BSR-Based Allele Calling Algorithm

cladeomatic

SNP population structure detection

htp_slurm_generator_scripts

Set of scripts for generating bash files for use with slurm

mob-typer

An in silico typing tool for plasmid mobility

mobclustering

Benchmarking methods for plasmid clustering

parsityper

Parsimonious genotype composition profiling using kmers

population_genetics

population genetics analysis tools and scripts

projectx

pipeline development for common processing workflow for nanopore and illumina data

salmonella_plasmid_dynamics

Code used to process interim files and visualize plasmid and gene associations

sgsa_array_classifier

sra-manuscript

Parsing tool for summarizing kraken-translate output