The recent plugin update to QIAGEN CLC Genomics version 21 (v21) includes new tools and database access within QIAGEN CLC Genomics Workbench. The new update enables you to:

• Import reads from MGI/BGI sequencers
• Import reads from Illumina sequencers, including the “i1” index fastq file, which is useful, for example, when analyzing Agilent UMI panels
• Access a new workflow for the SARS-CoV-2 ARTIC V3 panel on Illumina
• Redesign tools for upload of variant calls to QCI Interpret
• Create consensus sequences from variants using the new corresponding tool
• Perform haplotype calling and leverage genotype-aware tracks
• Perform TCR repertoire analysis for single-cell applications
• Identify and visualize viral integration sites into the human genome
• Leverage PICRUSt2-based support for functional inference or copy number normalization of 16S or ITS sequencing data
• Access Reference Virus DataBase (RVDB) directly from the software

Figure 1. The new Identify Viral Integration Sites tool in action, displaying evidence of a viral integration site in the host genome.

Features of new and updated QIAGEN CLC plugins

Biomedical Genomics Analysis plugin

• New BGI/MGI Sequencing Import tool
• New Custom Reads Illumina Sequencing Importer with extended options for fastq file import to support Agilent UMI panel data
  • It is now possible to import three fastq files with R1, R2 and i1 as paired reads where i1 is added in front of R1
• Import/export of clonotypes can now be used with VDJ tools
• Improved run time and performance of the Structural Variant Caller
• Upload to QCI Interpret and QCI Interpret Translational has been completely reworked, enabling easy authentication through a browser login
  • It allows the upload of a wider range of variants, including CNVs, fusions, inversions, TMB and MSI
  • These tools are server- and workflow enabled to allow easy automation of upload
• Create Consensus Sequences from Variants produces consensus sequences from a variant track and the matching reference
  • Low coverage regions can be masked
• New SARS CoV-2 ARTICv3 panel on Illumina analysis workflows

New Haplotype Calling plugin

This new plugin allows the detection, import, export and validation of variants with phasing information and delivers variant locus, allele variants, haplotype alleles and microhaplotypes.

QIAGEN CLC Single Cell Analysis Module 

• T Cell repertoire analysis is fully supported with new workflows and tools
• Doublet detection and removal is available from the QC for Single Cell tool
• The Create Expression Plot tool can now create violin plots

QIAGEN CLC Microbial Genomics Module

• Identify Viral Integration Sites tool makes it possible to detect viral integration events in host genomes from hybrid capture panel data
  • It provides a circular interactive and zoomable host/virus genome viewer that makes it possible to inspect integration events in detail
  • It features visualizations of coverage, unaligned-end coverage and broken-pair coverage, with CDS track overlays
  • Genes in close proximity are reported in a synchronized table
• The Analyze Viral Hybrid Capture Panel Data workflow identifies of the most prevalent viral species and its variants from a sample analyzed using hybrid capture technology
• PICRUSt2 is available for functional inference or copy number normalization of 16S or ITS sequencing data
• Food and Drug Administration’s (FDA) Reference Virus Data Base (RVDB) and the new QIAGEN Microbial Insights – Prokaryotic Taxonomy Database (QMI-PTDB) can now be downloaded using the Download Curated Microbial Reference Database tool

Learn more about the applications supported by our portfolio of QIAGEN CLC Genomics solutions, and request a consultation with one of our experts to help you find the right QIAGEN CLC toolset for your research goals.