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• Introduction
  • The concept of CLC Microbial Genomics Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Microbial template workflows
  • Taxonomic Analysis template workflows
    • Data QC and Remove Background Reads
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
    • QC, Assemble and Bin Pangenomes
  • Amplicon-Based Analysis template workflows
    • Data QC and OTU Clustering
    • Detect Amplicon Sequence Variants and Assign Taxonomies
    • Estimate Alpha and Beta Diversities
  • Typing and Epidemiology template workflows
    • Compare Variants Across Samples
    • Create MLST Scheme with Sequence Types
    • Map to Specified Reference
    • Type Among Multiple Species
    • Type a Known Species
  • QIAseq Analysis template workflows
    • Analyze QIAseq xHYB Viral Panel Data (Human host)
    • Find QIAseq xHYB AMR Markers (Human host)
  • QIAseq Panel Analysis Assistant
• De Novo Assemble Metagenome
• Amplicon-Based Analysis
  • Normalize OTU Table by Copy Number
  • Filter Samples Based on Number of Reads
  • OTU clustering
    • OTU clustering parameters
    • OTU clustering outputs
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Detect Amplicon Sequence Variants
    • Detect Amplicon Sequence Variants parameters
    • Detect Amplicon Sequence Variants output
    • Importing ASV abundance tables
  • Classify Long Read Amplicons
    • Classify Long Read Amplicons parameters
    • Classify Long Read Amplicons output
• Taxonomic Analysis
  • Contig Binning
    • Bin Pangenomes by Taxonomy
    • Bin Pangenomes by Sequence
  • Taxonomic Profiling
    • Taxonomic Profiling parameters
    • Taxonomic Profiling output
    • Taxonomic Profiling abundance table
  • Identify Viral Integration Sites
    • The Viral Integration Viewer
    • The Viral Integration Report
• Abundance Analysis
  • Merge Abundance Tables
  • Assign Taxonomies to Sequences in Abundance Table
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
    • Clustering of features and samples
    • The heat map view
    • Create heat map for specific taxonomic level
  • Add Metadata to Abundance Table
• Introduction to Typing and Epidemiology
• Find the best matching reference
  • Find Best Matches using K-mer Spectra
    • From samples best matches to a common reference for all
  • Find Best References using Read Mapping
    • The Find Best References using Read Mapping Report
• Phylogenetic trees using SNPs or k-mers
  • Create SNP Tree
    • SNP tree report
    • SNP tree
    • SNP Matrix
  • Create K-mer Tree
    • Visualization of K-mer Tree for identification of common reference
• MLST Scheme Tools
  • Getting started with the MLST Scheme tools
  • MLST Scheme Visualization and Management
  • Minimum Spanning Trees
    • The Minimum Spanning Tree view
    • Navigating the Tree view
    • The Layout panel
    • The Metadata panel
  • Type With MLST Scheme
    • Type With MLST Scheme results
    • The MLST Typing Result element
  • Add Typing Results to MLST Scheme
  • Identify MLST Scheme from Genomes
• Functional Analysis
  • Find Prokaryotic Genes
  • Annotate with BLAST
  • Annotate with DIAMOND
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Best DIAMOND Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
    • Functional profile abundance table
  • Infer Functional Profile
  • Identify Pathways
    • Called Pathways Result
    • The Identified Pathways View
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide Database
  • Find Resistance with ShortBRED
    • Resistance abundance table
• Databases for MLST Schemes
  • Create MLST Scheme
  • Download MLST Scheme
  • Import MLST Scheme
• Databases for Amplicon-Based Analysis
  • Download Amplicon-Based Reference Database
• Databases for Taxonomic Analysis
  • Download Curated Microbial Reference Database
    • Extracting a subset of a database
  • Download Custom Microbial Reference Database
    • Database Builder
  • Download Pathogen Reference Database
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download Ontology Database
    • The GO Database View
    • The EC Database View
  • Download Pathway Database
    • The Pathway Database
    • The Pathway View
  • Create DIAMOND Index
  • Import RNAcentral Database
  • Import PICRUSt2 Multiplication Table
• Databases for Drug Resistance Analysis
  • Download Resistance Database
    • ARES Database
• QIAseq 16S/ITS Demultiplexer
• Utility Tools
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
  • Result Metadata
    • Create a Result Metadata Table
    • Running an analysis directly from a Result Metadata Table
    • Extend Result Metadata Table
    • Use Genome as Result
• Legacy tools
  • Extract Regions from Tracks
  • Analyze Viral Hybrid Capture Panel Data
• Appendix
  • Using the Assembly ID annotation
• Bibliography

Getting started with the MLST Scheme tools

There are several ways to create MLST Schemes in the Microbial Genomics Module.

• Create MLST Scheme. Creates an MLST Scheme from sequence lists of reference genomes or assemblies with CDS annotations.
• Download MLST Scheme. Downloads existing MLST schemes from PubMLST.
• Import MLST Scheme. Imports an MLST scheme from a set of fasta files, sequence type info and optional locus metadata.

After a scheme has been obtained the following tools can be used together with the schemes.

• Type With MLST Scheme.
• Add Typing Results to MLST Scheme.

These tools are described in more detail in the following sections.

Finally, in order to be able to use the MLST Schemes outside of the Workbench, a MLST Scheme can be exported by clicking on the Export button and selecting MLST Scheme. To keep the data manageable, this will export the MLST Scheme into a single zip file containing two text files in tsv format, one with the sequence type definitions and sequence type metadata and the second file containing locus metadata, and one fasta file per locus, corresponding to the format used for importing MLST Schemes.

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