You asked for it by popular demand, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).
In this training, we’ll cover:
Description
This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.
Participants will learn the following:
o Download and install needed plugins.
o Import data required for the analysis.
o Run the de novo assembly workflow.
o For long reads, improve a de novo assembly by polishing with short, high-quality reads.
o Map reads to a reference and visualize an assembly.
o For long reads, correct raw long reads for further analysis.
o Use BLAST to investigate the contigs.
o Analyze and assemble contigs through Genome Finishing tools.
For RNA-seq data, you will learn how to:
• Import FASTQ files, cell matrix files and metadata and how to download references
• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.
• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, sankey plot and others
• Easily customize RNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways
Learn more about CLC or request a free trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-workbench-premium/
More and more biopharma and academic groups are looking to process a large number of samples simultaneously or for a quicker turnaround time. This webinar will introduce a flexible and powerful setup for running your NGS sequence analyses through servers or Amazon Web Services (AWS), depending on user preference. We will demonstrate how CLC Genomics Workbench can be used to customize workflows and send analyses for batch execution. We will also highlight analysis automation solutions, use of third-party dockers, audit trails and user management – all of which are available with the CLC Genomics Server software.
You will learn to:
• Customize template workflows to meet your NGS analysis requirements
• Set up a CLC Genomics Cloud environment on AWS
• Submit workflows to run on internal servers or AWS and retrieve results from these analyses
• Use third-party dockers and automate workflow execution
To learn more:
CLC Genomics Server: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/enterprise-ngs-solutions/qiagen-clc-genomics-server/?cmpid=CM_QDI_DISC_052024webinars
CLC Genomics Cloud Module: https://digitalinsights.qiagen.com/plugins/clc-cloud-module/?cmpid=CM_QDI_DISC_052024webinars
We’re excited to reveal many new improvements and enhancements to the latest release of QIAGEN CLC Genomics Workbench and its related plugins that significantly extend its value. Key improvements and new features in the new version (v24) include:
Figure 1. RNA-Seq volcano plot shows the relationship between fold changes and p-values. The reworked volcano plot allows for 1) different color gradients for positive and negative fold change values, 2) annotations, 3) legends and 4) customizable transparency of data points. Genes of interest can also be highlighted by setting thresholds.
Figure 2. Visualize and interact with spatial transcriptomics data.
Learn more about the applications supported by our portfolio of QIAGEN CLC Genomics software and request a consultation with one of our experts to help you find the right QIAGEN CLC toolset for your research goals.
This webinar will introduce users to the long read support plugin for Oxford Nanopore and PacBio sequencing reads in QIAGEN CLC Genomics Workbench.
Participants will learn the following:
• Download and install needed plugins.
• Import data required for the analysis.
• Long read de novo assembly.
• Map reads to a reference and visualize an assembly.
• Use BLAST to investigate the contigs.
• Additional long read tools: polish with short reads, structural variant calling.
• Genome finishing tools: analyze and assemble contigs
• Analytical tools: RNA-seq analysis for long reads, classify long read amplicons for metagenomics.
Do you ever get stuck processing raw FASTQ data or cell matrix data from your RNA-seq, scRNA-seq or other NGS assays using? Are you interested in creating a differential expression table that’s compatible with the QIAGEN Ingenuity Pathway Analysis (IPA) software you use? In this training, you’ll learn how to use QIAGEN CLC Genomics Workbench to easily process your FASTQ files and generate differential expression tables without using command line tools. We’ll also explore how you can generate other desired outputs, such as volcano plots, heatmaps, PCA/PCOA plots and more.
You can delve into more information about QIAGEN CLC Genomics Workbench here:
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-genomics-workbench/
In this webinar, we’ll introduce algorithms required to perform data analysis for resequencing next-generation sequencing data. Together, we’ll explore:
• Read mapper
• Variant callers
• Annotations and filters
• Genome Browser
Bring any questions you may have, and we will answer them during the webinar.
QIAGEN CLC Genomics Workbench provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization through SNP and K-mer trees using NGS data, and antimicrobial resistance characterization. CLC Genomics Workbench is widely used for analyses of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.
We’ll cover these topics in the training:
I. Overview of different tools within MGM application and research areas supported
II. Focused review of isolate typing and characterization
a. Importing data
b. Utilization of metadata
c. Downloading and managing references
i. Database of Isolates/ Resistances/ MLST
d. Walk through of Type a Known Species workflow
i. Review details for each Isolate
e. Creating SNP profiles to specific reference
f. Generate a SNP tree for isolate comparison
g. Export tabular and high-quality graphical outputs in wide range of file formats
Circulating tumor cells (CTCs) are cells that leave the primary tumor and are intravasated into the blood circulation system. A subset of those make it to other organs and are responsible for metastasis. iCellate’s CellMate platform is a CTC-based liquid biopsy for cancer cell enrichment, detection, and biomarker analysis via a simple blood draw.
In this seminar, you’ll learn:
