CLC Microbial Genomics Module 3.0

Taxonomic Profiling using Whole Metagenomic 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.

Our Taxonomic Profiling tool offers taxonomic analysis of Whole metagenome shotgun sequencing data. Get started easily with two preconfigured workflows for data QC and taxonomic profiling. Easy-to-use statistical tools enable comparison of microbial communities across many samples.

In our new release, we have updated the tool to run with improved sensitivity for taxonomic profiling and abundance estimation of whole metagenome shotgun data.

  • Increased sensitivity in taxonomic profiling
  • Improved abundance estimation – in particular of species occurring at low frequency
  • Testing for differential abundance now allows the inclusion of control groups

Stay tuned for more improvements in 2018!

 

 

Pathogen Tracing Using Genome-wide SNP Comparison

Pathogen surveillance and outbreak analysis is key to prevent and control disease outbreak or re- emergence. Sufficient resolution is crucial to unravel the chain of transmissions when comparing closely related isolates. Whole genome sequencing is becoming a standard for surveillance and epidemiological investigation of pathogen outbreaks, permitting transmission analysis with maximum discriminatory power.

Our tools provide robust and streamlined processing of NGS data, offer intuitive interpretation of the analysis results and scale with fluctuating sample loads. Outbreak investigation is visually guided by the reconstruction of interactive phylogenetic trees helping investigators to delineate pathogen transmission in the context of epidemiologically relevant metadata.

In our new release, we have updated the tool for genome-wide SNP analysis to provide phylogenies at highest accuracy.

  • Construct SNP trees or MNV (multi-nucleotide variant) trees with the Maximum Likelihood reconstruction algorithm for improved accuracy
  • New feature: Matrix displaying the identified SNP’s between any pair of samples
  • New feature: Isolate SNP strings can be exported to VCF format and compared in a Genome Browser (track list) view

 

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