StaPH-B

Staramr scans bacterial genome contigs for AMR genes and plasmids

Convert various sequence formats to FASTA

NCBI Datasets: easily gather data from across NCBI databases

Scan contig files against traditional PubMLST typing schemes (tool from T. Seemann)

PopPUNK: POPulation Partitioning Using Nucleotide Kmers

Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset

BBTools suite of tools from Joint Genome Institute

Collection of tools and libraries for using data in the INSDC Sequence Read Archives

htslib: A C library for reading/writing high-throughput sequencing data

Tools (written in C using htslib) for manipulating next-generation sequencing data

Variant calling & manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF

Automated prokaryotic genome annotation tool

Kraken2: Taxonomic sequence classifier. Some images with a kraken2 db and some w/out

Salmonella serotyping from genome sequencing data

Find acquired AMR genes and some point mutations in protein or assembled nucleotide sequences

Screen genome assemblies of Klebsiella pneumoniae and Kp species complex (KpSC)