Molecular Microbiology and Infection Unit

Docker image of the chewBBACA software for wg/cgMLST

Assembled Genomes Compressor.

Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.

Mass screening of contigs for antimicrobial and virulence genes

Scan contig files against PubMLST typing schemes

INNUENDO pipeline for quality control of reads and de novo assembly

MIDAS estimates strain-level genomic variation from metagenomic data

seq_typing - Determines which reference sequence is more likely to be present in a given sample

Prokka annotates bacterial, archaeal and viral genomes

Interactive toolkit for assembly and analysis of restriction-site associated genomic data sets

Stacks is a software for building loci from short-read sequences

In silico typing of Neisseria meningitidis contigs

Docker container with Snippy software

St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines

Blast+ for LOBO cluster performance testing

rPinecone defines sub-lineages within a bacterial clonal expansion via a phylogenetic tree.

Parsnp aligns the core genome of hundreds of bacterial genomes within a few minutes to few hours

Docker image with basic Ubuntu tools

Typing of the emm gene of Streptococcus pyogenes (and other Streptococci)

SeqSero2 is a pipeline for Salmonella serotype determination from raw reads or genome assemblies

Get fastq files from ENA using Run IDs

breseq is a pipeline for finding mutations relative to a reference sequence in NGS data

Base image for assemblerflow templates

Strategic Kmer Extension for Scrupulous Assemblies

In silico pathogenic typing directly from raw Illumina reads

Reads mapping against target sequences, checking mapping and consensus sequences production

SISTR: Salmonella serovar predictions from whole-genome sequence assemblies

Automated genome assembly improvement and variant detection tool

A flexible read trimming tool for Illumina NGS data

A quality control tool for high throughput sequence data.