Microbial genomics Tools

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.

ISMapper searches for IS positions in sequence data using paired end Illumina short reads, an IS query/queries of interest and a reference genome. ISMapper reports the IS positions it has found in each isolate, relative to the provided reference genome.

InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

Kover is an out-of-core implementation of rule-based machine learning algorithms that has been tailored for genomic biomarker discovery. It produces highly interpretable models, based on k-mers, that explicitly highlight genotype-to-phenotype associations.

LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies The MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location.

MashTree is a fast command-line tool for creating phylogenetic trees from genome assemblies or raw reads using Mash distances, enabling rapid whole-genome phylogeny estimation without traditional sequence alignment.

MetaCHIP is a horizontal gene transfer (HGT) identification pipeline that combines best-match and phylogenetic approaches to detect community-level HGT events in microbial genomes.

Mykrobe is a tool for rapid antibiotic resistance prediction and species identification in bacterial genomes using a reference-free approach based on De Bruijn graphs, primarily designed for Mycobacterium tuberculosis and Staphylococcus aureus.

NCBI AMRFinderPlus is a tool for identifying acquired antimicrobial resistance genes, stress response genes, and virulence genes in bacterial genomes and proteins using the NCBI Reference Gene Catalog and curated expert-validated database.

Antimicrobial Resistance Identification By Assembly

Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

Dnaapler is a simple tool that reorients complete circular microbial genomes.

Assemble bacterial isolate genomes from Nanopore reads. Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy.

mlst is a command-line tool that scans contig files against PubMLST typing schemes to perform in silico multi-locus sequence typing (MLST), enabling rapid identification and typing of bacterial isolates.