:zap: :aquarius: Rapid prokaryotic genome annotation

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

A flexible pipeline for complete analysis of bacterial genomes

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

Bioinformatics tool to find integrons in bacterial genomes

Simple bacterial assembly and annotation pipeline

Split Kmer Analysis

A genome diagram generator for microbes and organelles

Machine-learning-based general bacterial promoter prediction tool.

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

Fast k-mer based tool for multi locus sequence typing (MLST)

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

Phage-Host Interaction Search Tool

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

Combining de novo and reference-guided assembly with Scaffold_builder

genome sized sequences clustering

Various scripts for efficient processing of 10k Salmonella genomes

PowerBacGWAS: Power calculations for Bacterial GWAS

Tool intended to pull out sequences and annotations between insertion sites specified by the user.

Bioinformatics pipeline for nanopore sequencing data

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

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

PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

SNP and variant calling pipeline for bacteria