• Manuals

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• Introduction to CLC Microbial Genomics Module
  • The concept of CLC Microbial Genomics Module
  • Contact information
• System requirements and installation
  • System requirements
  • Installation of modules
  • Workbench Licenses
  • Uninstalling modules
  • Server Licenses
• Introduction to Metagenomics
• Amplicon-based OTU clustering
  • Filter Samples Based on the Number of Reads
  • OTU clustering
    • OTU clustering parameters
    • OTU clustering tool outputs
    • Visualization of OTU abundance tables
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Amplicon-Based OTU Clustering Workflows
    • Data QC and OTU Clustering workflow
    • Estimate Alpha and Beta Diversities workflow
• Taxonomic Analysis
  • Taxonomic Profiling
    • Taxonomic profiling abundance table
    • Taxonomic Profiling report
  • Workflows
    • Data QC and Clean Host DNA
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
• Functional analysis
  • De Novo Assemble Metagenome
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
• Abundance analysis
  • Merge Abundance Tables
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
  • Add Metadata to Abundance Table
  • Convert Abundance Table to Experiment
• Introduction to Typing and Epidemiology (beta)
• Handling of metadata and analysis results
  • Importing Metadata Tables
  • Associating data elements with metadata
  • Create a Result Metadata Table
  • Running an analysis directly from a Result Metadata Table
    • Filtering in Result Metadata Table
    • Filtering in a SNP-Tree creation scenario
  • Add to Result Metadata Table
  • Use Genome as Result
• Workflow templates
  • Map to Specified Reference
    • How to run the Map to Specified Reference workflow on a single sample:
    • How to run the Map to Specified Reference workflow on a batch of samples:
  • Type Among Multiple Species
    • Preliminary steps to run the Type Multiple Species workflow
    • How to run the Type among Multiple Species workflow for a single sample
    • Example of results obtained using the Type among Multiple Species workflow
    • How to run the Type among Multiple Species workflow on a batch of samples:
  • Type a Known Species
    • Preliminary steps to run the Type a Known Species workflow
    • How to run the Type a Known Species workflow for a single sample
    • Example of results obtained using the Type a Known Species workflow
    • How to run the Type a Known Species workflow on a batch of samples:
  • Extract Regions from Tracks
• Find the best matching reference
  • Find Best Matches using K-mer Spectra
  • From samples best matches to a common reference for all
• Resistance typing
  • Find Resistance
• Phylogenetic trees using SNPs or k-mers
  • Create SNP Tree
    • SNP tree output report
    • Visualization of SNP Tree including metadata and analysis result metadata
    • SNP Tree Variants editor viewer
  • Create K-mer Tree
    • Visualization of K-mer Tree for identification of common reference
• NGS MLST
  • Schemes visualization and management
  • Identify MLST
  • Identify MLST Scheme from Genomes
• Working with databases
  • Create Microbial Reference Database
  • Download Pathogen Reference Database
    • Extracting a subset of a database
    • Download Pathogen Reference Database output report
  • Set Up Microbial Reference Database
  • Download Database for Find Resistance
  • Set Up Gene Database
  • Download Amplicon-Based Reference Database
  • Set Up Amplicon-Based Reference Database
  • Download GO Database
  • NGS MLST Databases
    • Download MLST Schemes
    • Download other MLST Schemes
    • Create MLST Schemes
    • Add NGS MLST Report to Scheme
    • Merge MLST Schemes
    • Add Sequences to MLST Schemes
• Legacy tools
  • Optional Merge Paired Reads
  • Fixed Length Trimming
• Licensing requirements for the CLC Microbial Genomics Module
  • Workbenches licenses
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure license server connection
    • Download a static license on a non-networked computer
  • Server licenses
    • Static license installation
    • Windows license download
    • Mac OS license download
    • Linux license download
    • Download a static license on a non-networked machine
    • Network license installation
• Bibliography

Resistance typing

Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. The Find Resistance tool may be used for resistance typing of pre-assembled, complete or partial genomes simple contig sequences assembled using the de novo assembly algorithm of CLC Genomics Workbench (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=De_novo_assembly.html). Alternatively, use the Type a Known Species or Type among Multiple Species template workflows as described in the chapter Workflow templates.

The Find Resistance tool is inspired by [Zankari et al., 2012] and uses BLAST for identification of acquired antimicrobial resistance genes within whole-genome sequencing (WGS) data.

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Subsections

• Find Resistance

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