Bakta

EcoliTyper is a revolutionary bioinformatics pipeline that eliminates workflow fragmentation in E. coli genomic surveillance. By integrating nine core analyses into a single automated workflow, EcoliTyper transforms disconnected genomic data into coherent biological narratives with actionable public health intelligence. It is a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli, perfect for clinical microbiology, outbreak investigations, and genomic research.

Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

JavaScript genome browser that is highly customizable via plugins and track customizations.

Annotate a VCF with other VCFs/BEDs/tabixed files.

Pairwise SNP distance matrix from a FASTA sequence alignment

D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.