RepEnrich

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

Toolkit for processing sequences in FASTA/Q formats.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Open-source, platform-independent, community-supported software for describing and comparing microbial communities

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.