Microbial Genomics and Metagenomics Analysis Tools

Working with metagenomic and microbial analyses? Augment your Workbench with our genomics toolset designed for microbial data. 

Uncover critical correlations among microbiota, metagenomes and hosts

Navigate complex metagenomic data through workflows for gene finding, annotation, taxonomic and functional microbiome analysis

Access custom and public databases

Navigate complex microbial genomics data

Whether you’re focused on public health epidemiology, clinical microbiology or other genomics research, we have the tools you need to study bacterial, fungal and viral genomes.

Antimicrobial resistance (AMR)
Detect and analyze AMR genes and markers
Identify resistances, acquired genes and mutations in metagenomic or isolate NGS samples
Microbiome and metagenomics profiling
Analyze amplicon and whole metagenome sequencing data
Analyze short and long read 16S, 18S and ITS amplicon data
De novo assembly and contig binning and gene finding
Explore and compare taxonomic profiles
Pathogen typing and outbreak analysis
MLST-, cgMLST-, wgMLST- or SNP-based analyses
Assembly-free K-mer-based strain typing
Get taxonomy and reference genomes for microbial isolates
Investigate pathogens and outbreaks with K-mer trees and whole genome SNP trees
Database connections

Leading AMR gene databases QMI-AR, CARD, ResFinder, PointFinder and the QIAGEN Microbial Insights AR database, plus Greengenes, Silva, UNITE and more

Marker databases derived from QMI-AR, CARD and ARG-ANNOT
Genome reference databases derived from NCBI microbial data

Easily manage and analyze your whole-genome data

Compare, explore and visualize genomes and their evolutionary relations, in one handy tool. Supports standard whole-genome alignments formats (MAF and XMFA).

  • Align multiple genomes and extract their sequence alignments
  • Transfer annotations from reference genomes to other alignment sequences
  • Create evolutionary trees, heat maps and whole-genome dot plots

Augment your Workbench's microbial capabilities

Our suite of CLC modules and plugins has you covered, from fine-grain AMR gene analysis to whole-genome assembly. 
Looking for inspiration?
Browse our collection to see how to accelerate your microbial and viral research.
See all resources
Our solutions at work
Start making sense of your complex microbial genomics data.
Learn more
Antimicrobial resistance and multi-locus sequence typing
See how to kickstart your antimicrobial resistance research.
Watch the webinar
Sample to Insight
linkedin facebook pinterest youtube rss twitter instagram facebook-blank rss-blank linkedin-blank pinterest youtube twitter instagram
This site is registered on wpml.org as a development site. Switch to a production site key to remove this banner.