Bio-DB-HTS

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

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.