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.
The recently released tutorial for handling long, error-prone reads in QIAGEN CLC Genomics Workbench 20 focuses on how to perform hybrid assembly with long, error-prone reads and high-quality, short reads. The tutorial teaches you how to assess the quality of the assembly using a reference and the Whole Genome Alignment plugin (read our blog post to learn more).
The hybrid assembly for a supplied dataset is easily carried out following a simple workflow (Figure 1).
The first step is to run the De Novo Assemble Long Reads (beta) tool resulting in an almost perfect assembly using only Oxford Nanopore reads, as assessed by evaluating the alignment percentage (AP) of 99.61% and average nucleotide identity (ANI) of 99.92% after alignment to the expected reference. After contig polishing with the supplied Illumina reads using the Polish with Reads (beta) tool, these quality measures are improved to AP 99.81% and ANI 99.93%. A single misassembly is identified along the way (Figure 2), highlighting when it becomes necessary to correct the reads before assembly.
After read correction and assembly, the misassembly disappears (Figure 3).
The reduction of errors in the reads can be visualized in a read mapping to the reference genome using the Map Long Reads to Reference (beta) tool (Figure 4).
Found this blog useful? Stay tuned for regular blog posts, full of valuable information!
The QIAGEN CLC Genomics Workbench now enables analysis of uncorrected long reads from Oxford Nanopore and PacBio using a newly developed plugin that provides seamless integration with other QIAGEN CLC products. The Long Read Support plugin builds on established state-of-the-art pipelines for read mapping, read error correction, de novo assembly and contig polishing that are made available through the user-friendly workbench graphical user interface (GUI). No command-line or code compilation is needed. Benefits of the Long Read Support plugin include:
Find out the details in our scientific poster and learn more about the Long Read Support plugin, QIAGEN CLC Genomics Workbench and QIAGEN CLC Microbial Genomics Module. Learn more about de novo assembly using long reads and short read polishing in this tutorial.
