bacteria

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Build a partitioned pangenome graph from microbial genomes

💾 📃 "Reads to report" for public health and clinical microbiology

Pan-genome wide association studies

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

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

SEER, reimplemented in python 🐍🔮

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

A scalable bacterial genome assembly, annotation and analysis pipeline

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

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

A bioinformatic toolkit to align genome assemblies into pangenome graphs

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

sequence element (kmer) enrichment analysis

Accurate, resource-frugal and deterministic DNA sequence classifier.

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

PLSDB pipeline to collect bacterial plasmids from NCBI

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