CLC Microbial Genomics Module 2.0

Identify microbes with strain level accuracy in metagenomics data

When investigating microbial communities, some of the main questions include, which microorganisms are present and how abundant are they? Shotgun metagenomics sequencing is a powerful tool for investigating bio-diversity of microbial communities.

Common challenges include unwanted signals from host DNA which can reduce the sensitivity at which the microorganisms can be detected. In addition, large data volumes and the complex data structure of metagenomics data further complicate computational analysis.
 
 

Taxonomic profiling of whole shotgun metagenomic data

The new tool Taxonomic Profiling offers taxonomic analysis of Whole metagenome shotgun sequencing data. Start metagenome analysis on day one with two preconfigured workflows for data QC and taxonomic profiling. Easy to use Statistical tools enable comparison of microbial communities across many samples.

  • Filter out data contamination originating from host DNA
  • Merge abundance tables for direct comparison of diversity metrics
  • Data visualisation with stacked bar charts, stacked area charts, sunburst charts and heat-maps
  • User-friendly statistical tools deliver class-leading performance for Alpha and Beta diversity estimation, PERMANOVA Analysis and Differential Abundance Analysis

 

 


 
 

Reference genome database – manage database content for highest precision

Using the right reference data is crucial for accurate taxonomic profiling. But bigger is not always better – database size and content affect computer resource requirements and specificity.
The new tool Create Microbial Reference Database is designed to overcome these common challenges in metagenome analysis.

From discovery to routine use

Managing reference data is crucial for translating a discovery application into routine use. For exploring the microbial diversity in novel sample types use a comprehensive database. For highest precision and faster turn-around time in routine use, simply remove irrelevant taxa from the reference database.

The new tool Create Microbial Reference Database allows users to build customised reference genome databases for use in taxonomic profiling and microbial isolate typing.

  • Direct import of microbial genomes from NCBI. Getting started is easy – three built-in quick-select options provide access to subsets of NCBI’s broad microbial content.
  • With filters for taxonomy and assembly-quality, database contents can be optimised by the user. Remove low quality assemblies for higher confidence taxonomic assignments, or minimise computer resources and analysis time by reducing redundancy of database entries.
  • A table provides an overview of covered taxonomic range, assembly status and size of incuded genomes.
  • Monitor predicted file size of database during the design, before the download begins.

 
 

New users get started faster thanks to preconfigured Workflows

The latest release features two new preconfigured and easy-to-use Workflows that combine the most important steps of taxonomic microbiome profiling: Data QC and removal of contamination, taxonomic profiling of one or many samples, and downstream statistical analysis.

New Workflows:

  • Data QC and Clean Host DNA
  • Merge and Estimate Alpha and Beta Diversity

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