CLC Microbial Genomics Module

Analysis of microbial genomics and metagenomics made easy!

CLC Microbial Genomics Module offers tools and workflows for microbiome analysis, further extending the broad range of supported NGS applications.

The Taxonomic Profiling tool offers taxonomic analysis of whole metagenome shotgun sequencing data. Start metagenome analysis on day one with two preconfigured workflows for data QC, removal of contaminating data originating from host DNA, taxonomic profiling, and estimation of alpha and beta diversity. Easy-to-use statistical tools enable comparison of microbial communities across many samples.

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

 

Supported features

Microbiome Profiling

  • De novo or reference based OTU-clustering of 16S rRNA or other amplicon data.
  • Easy access to common reference databases such as Greengenes, Silva and UNITE.
  • Taxonomic profiling of metagenomic data.
  • Custom-built genome reference database by direct import of microbial genomes from NCBI provide highest precision taxonomic assignment.
  • Metagenome de novo assembly and functional profiling of microbiomes using PFAM, Gene Ontology and BLAST.
  • Stacked bar charts, area charts, sunburst charts and heat-maps to explore and compare the taxonomic composition of samples, or sample groups.
  • User-friendly statistical tools deliver class-leading performance for Alpha and Beta diversity estimation, PERMANOVA Analysis and Differential Abundance Analysis.

 

Pathogen Typing and Outbreak Analysis

  • Automated identification and characterisation of microbes using whole genome data. A single easy to use Workflow reports NGS-MLST, taxonomy, closest known reference genome and antimicrobial resistance genes for microbial isolates.
  • K-mer trees and whole genome SNP trees for accurate outbreak investigation and source tracking of pathogens.
  • Assembly of microbial genomes by short read and hybrid assembly, with support for error-correction and assembly of PacBio reads.
  • Find genes with the MetaGeneMark plugin and annotate with PFAM, Gene Ontology and BLAST.

 

 

Read the latest improvements here.

 

Find out more

Downloads


Plugin Manual

Plugin Download

Download plugin

Download CLC Microbial Genomics Module


Version

Platform support

Download

4.1.0

CLC Genomics Workbench


 [12.0]

3.6.1

Biomedical Genomics Workbench


 [5.0.2, 5.0.1]

CLC Genomics Workbench


 [11.0.2, 11.0.1]

3.0.0

Biomedical Genomics Workbench


 [5.0.0]

CLC Genomics Workbench


 [11.0.0]

2.5.5

Biomedical Genomics Workbench


 [4.1.3, 4.1.2]

CLC Genomics Workbench


 [10.1.3, 10.1.2]

2.5.1

Biomedical Genomics Workbench


 [4.1.1, 4.1.0]

CLC Genomics Workbench


 [10.1.1, 10.1.0]

2.0.0

Biomedical Genomics Workbench


 [4.0]

CLC Genomics Workbench


 [10.0.1, 10.0]

1.6.2

Biomedical Genomics Workbench


 [3.5.4]

CLC Genomics Workbench


 [9.5.4]

1.6.1

Biomedical Genomics Workbench


 [3.5.3, 3.5.2, 3.5.1, 3.5]

CLC Genomics Workbench


 [9.5.3, 9.5.2, 9.5.1, 9.5]

1.5.1

Biomedical Genomics Workbench


 [3.0.1, 3.0]

CLC Genomics Workbench


 [9.0.1, 9.0]

1.4.1

Biomedical Genomics Workbench


 [2.5.4, 2.5.3]

CLC Genomics Workbench


 [8.5.4, 8.5.3]

1.2.2

Biomedical Genomics Workbench


 [2.5.2]

CLC Genomics Workbench


 [8.5.2]

1.2.1

Biomedical Genomics Workbench


 [2.5.1, 2.5]

CLC Genomics Workbench


 [8.5.1, 8.5]

1.0

Biomedical Genomics Workbench


 [2.1.2, 2.1.1, 2.1]

CLC Genomics Workbench


 [8.0.3, 8.0.2, 8.0.1, 8.0]

Server plugin Downloads

Download plugin

Download CLC Microbial Genomics Server Extension


Version

Platform support

Download

4.1.0

CLC Genomics Server


 [11.0]

3.6.1

Biomedical Genomics Server Solution


 [10.0.2, 10.0.1]

CLC Genomics Server


 [10.0.2, 10.0.1]

3.0.0

Biomedical Genomics Server Solution


 [10.0]

CLC Genomics Server


 [10.0.0]

2.5.5

Biomedical Genomics Server Solution


 [9.1.3, 9.1.2]

CLC Genomics Server


 [9.1.3, 9.1.2]

2.5.1

Biomedical Genomics Server Solution


 [9.1.1, 9.1]

CLC Genomics Server


 [9.1.1, 9.1.0]

2.0.0

Biomedical Genomics Server Solution


 [9.0]

CLC Genomics Server


 [9.0]

1.6.2

Biomedical Genomics Server Solution


 [8.5.4]

CLC Genomics Server


 [8.5.4]

1.6.1

Biomedical Genomics Server Solution


 [8.5.3, 8.5.2, 8.5.1, 8.5]

CLC Genomics Server


 [8.5.3, 8.5.2, 8.5.1, 8.5]

1.5.1

Biomedical Genomics Server Solution


 [8.0.1, 8.0]

CLC Genomics Server


 [8.0.1, 8.0]

1.4.1

Biomedical Genomics Server Solution


 [7.5.4, 7.5.3]

CLC Genomics Server


 [7.5.4, 7.5.3]

1.2.2

Biomedical Genomics Server Solution


 [7.5.2]

CLC Genomics Server


 [7.5.2]

1.2.1

Biomedical Genomics Server Solution


 [7.5.1, 7.5]

CLC Genomics Server


 [7.5.1, 7.5]

1.0

Biomedical Genomics Server Solution


 [7.0.3, 7.0.2, 7.0.1, 7.0]

CLC Genomics Server


 [7.0.3, 7.0.2, 7.0.1, 7.0]

Step 1 - About you

Step 2 - Organizational details

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