Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Build a partitioned pangenome graph from microbial genomes

Pan-genome wide association studies

BSR-Based Allele Calling Algorithm

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

SEER, reimplemented in python 🐍🔮

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

A scalable bacterial genome assembly, annotation and analysis pipeline

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

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

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

sequence element (kmer) enrichment analysis

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

PLSDB pipeline to collect bacterial plasmids from NCBI

Accurate, resource-frugal and deterministic DNA sequence classifier.

A simulation of protozoan behavior and evolution

Identify phage regions in bacterial genomes for masking purposes

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Order and orientation of complete bacterial genomes

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS