![]() ![]() The smaller the chimeric cost, the more likely it is that a read is deemed chimeric setting it too high decreases the chimeric detection. Therefore without the chimera crossover cost, the constructed alignments difference score can only be 3% at most. If the best match that can be constructed has at least one crossover and the "constructed alignment" is at least as good as the "similarity percentage", then the read is being considered chimeric.īy default, the similarity percentage parameter is set to 97% in the OTU Clustering tool. To speed up the chimera crossover detection algorithm, the read is not aligned to all OTUs but only to some "promising candidates" found via a k-mer search. If a read cannot be put into an already existing OTU (because there is no single OTU that is similar enough, i.e., within 97% similarity), the algorithm tries to optimize the alignment score by allowing to "cross over" from one database reference to another at a cost (the chimera crossover cost). The tool aligns the reads to all OTUs to create an "alignment score" for each OTU. Microbial Genomics Module ( ) | Metagenomics ( ) | Amplicon-based OTU clustering ( ) | OTU clustering ( ). The OTU clustering tool clusters a collection of reads to operational taxonomy units. Download a static license on a non-networked machine.Download a static license on a non-networked computer.Download a license using a license order ID.Licensing requirements for the CLC Microbial Genomics Module.Set Up Amplicon-Based Reference Database.Download Amplicon-Based Reference Database.Download Pathogen Reference Database output report.Visualization of K-mer Tree for identification of common reference.Visualization of SNP Tree including metadata and analysis result metadata.Phylogenetic trees using SNPs or k-mers.From samples best matches to a common reference for all.How to run the Type a Known Species workflow on a batch of samples:.Example of results obtained using the Type a Known Species workflow.How to run the Type a Known Species workflow for a single sample.Preliminary steps to run the Type a Known Species workflow.How to run the Type among Multiple Species workflow on a batch of samples:.Example of results obtained using the Type among Multiple Species workflow.How to run the Type among Multiple Species workflow for a single sample.Preliminary steps to run the Type Multiple Species workflow.How to run the Map to Specified Reference workflow on a batch of samples:.How to run the Map to Specified Reference workflow on a single sample:.Filtering in a SNP-Tree creation scenario.Running an analysis directly from a Result Metadata Table.Associating data elements with metadata.Handling of metadata and analysis results.Introduction to Typing and Epidemiology (beta).Merge and Estimate Alpha and Beta diversities.Estimate Alpha and Beta Diversities workflow.Amplicon-Based OTU Clustering Workflows.Importing and exporting OTU abundance tables.Filter Samples Based on the Number of Reads.The concept of CLC Microbial Genomics Module.Introduction to CLC Microbial Genomics Module. ![]()
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