We are excited to share with you news of the new QIAGEN CLC Genomics version 22, which offers you many improvements and new features, including:

• Example workflows provided under the new Template Workflows area of the Toolbox
• Expanded range of tools for grouping and describing sequences in sequence lists
• Support for NGS data import from Amazon S3 and Illumina BaseSpace
• Import data generated by MGI/BGI systems

See our latest improvements page for information about all the updates in this CLC Genomics Workbench release.

See the latest improvements page for information about all the updates in this CLC Genomics Server release.

Plugins and Modules

Many plugins and modules have new features and improvements. Highlights include:

• Single-cell ATAC-seq and RNA velocity analysis in QIAGEN CLC Single Cell Analysis Module
• Fast long-read assembler for Oxford Nanopore and PacBio reads lets you assemble both small, circular bacterial genomes or large eukaryotic genomes with the Long Reads Support plugin (beta)
• Import RNA-seq expression data in matrix format with the Ingenuity Pathway Analysis (IPA) plugin - to help you quickly get from count data through differential analysis to data interpretation (requires a separate license to QIAGEN IPA)
• Support for methylation profiling with the Predict Methylation Profile (beta) tool in Biomedical Genomics Analysis plugin

Discover all QIAGEN CLC plugins here.

New Application Notes

Assembly and annotation of plastid genomes using QIAGEN CLC Genomics Workbench

RNA-seq analysis using long and short reads from pathogen-infected plant tissues

Improving structural annotation in complex genomes with QIAGEN CLC Genomics Workbench

A strategy for evaluating genomic assemblies in QIAGEN CLC Genomics Workbench

Discover additional application notes here.

New Tutorials

Immune Repertoire Analysis using QIAseq Immune Repertoire panels

Analysis of Viral Hybrid Panel Data and Identification of Viral Integration Sites

Creating and using annotated sequences as microbial reference data

Explore additional tutorials here.

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.

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.