drhchen

snpless-nf

snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.

pangenome_variation

Run several analysis on bacterial genomes

hogwash

Three bacterial GWAS methods all rolled into one easy-to-use R package

BacDist

Snakemake pipeline for bacterial SNP distance and phylogeny analysis

sketchy

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

zDB

zDB: comparative bacterial genomics made easy

SigmoID

A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes

core-genome-alignment

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

snp_calling_scripts

Collection of scripts for bacterial SNP calling

BacGWASim

A Simulator for Bacterial Machine learning and Genome-Wide Association Studies

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

phandangoExampleData

The data underlying the examples on phandango.net

tormes

Making whole bacterial genome sequencing data analysis easy

hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

mashtree

:deciduous_tree: Create a tree using Mash distances

CRKP_ST11_KL64

Genome-centric Analysis Workflow for the CRKP_ST11_KL64 paper

hzcdc

Sibelia

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

transcluster

Infer transmission clusters from SNP and timing data

FastANI

Fast Whole-Genome Similarity (ANI) Estimation

snp-sites

Finds SNP sites from a multi-FASTA alignment file

rhierbaps

rhierbaps: R implementation of hierBAPS

lung_cancer_microbiome

HGT-Finder

Program for finding horizontal gene transfer using BLAST result

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Genomic_and_Patient_Transfer_Analyasis_of_Resistant_Bacteria

Active surveillance of newly-admitted nursing home patients for colonization of antibiotic-resistant bacteria reveals that multiple lineages have spread across southeast Michigan healthcare networks.

plascad

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

THE-BIOHACKING-BIBLE

:pill: :pill: :pill: :pill: :pill: Lots of resources on the world of Biohacking, Genetic Editing, Biology, Bacteria, DNA, CRISPR, Cas9, Plasmids, Antibiotics, PCR, and moooreeeee... :pill: :pill: :pill: :pill: :pill: IN CELL WE TRUST!!! :pill: :pill: :pill: :pill: :pill:

RecentHGT

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

MetaCHIP

Horizontal gene transfer (HGT) identification pipeline