CLC GENOMICS WORKBENCH ASSEMBLY MANUAL

To reassemble all annotated regions, the tool can be run from the Workbench Toolbox. This adjusts the read mapping and makes changes in the consensus sequence based on the reads in the selected region. Misassembled regions and other problematic areas can be reassembled using the Reassemble regions tool. You can select an area of a contig and perform a range of actions, as described in the manual: These annotations can then be used to pinpoint misassembled regions during visual inspection of the alignments. It identifies and annotates problematic regions in the de novo assembly. The tools listing below are generally used in combination with the Align Contigs tool, described above.ĭetect misassemblies by analyzing reads mapped to contigs using the Analyze Contigs tool. Improving Correctness (manual editing tools)

CLC GENOMICS WORKBENCH ASSEMBLY MANUAL

The Align Contigs tool is the gateway to downstream visual inspection and manual editing of the contigs.įrom the output of Align Contigs tool, one can join, split and edit contig sequences, view the reads mapped to a given contig, remap all mapped reads to one or more contigs, and replace all mapped reads with reads from one or more datasets.įurther information can be found in the manual: It also determines the orientation and location of the contigs relative to the reference, which allows the identification of possible misassemblies, repeats, and overlaps between contigs. This helps identify areas of the genome not covered by the assembled contigs. The Align Contigs tool can be used to map your contigs to a related reference, or, if no such reference is available, to the contigs themselves. Automatic contig joining can be done using long reads, a closely related reference, paired read data or by aligning contigs to each other.įurther details can be found in the manual: The number of contigs in the assembly can be reduced by joining contigs likely to represent one contiguous sequence using the Join Contigs tool. In the Map Reads to Contigs wizard, select the output option Create stand-alone read mappings (not the default). If you do not already have such a mapping, you will need to take your unfinished genome contigs and map the reads to these using the Map Reads to Contigs tool. In the Navigation Area, stand-alone read mappings have icons that look like those shown below: Most of the tools provided by the CLC Genome Finishing Module take stand-alone read mappings as input. In addition, PacBio reads can be assembled using the PacBio De Novo Assembly Pipeline delivered by the CLC Genome Finishing Module, and PacBio and Oxford Nanopore reads can be assembled using the De Novo Assemble Long Reads tool delivered by the Long Read Support (beta) plugin. To create an initial assembly, the De Novo Assembly tool of the CLC Genomics Workbench can be used. Getting started (create an assembly and map the reads back to the contigs) This page presents a summary of the facilities available using tools delivered by the CLC Genome Finishing Module in an order reflecting the order they might be used in practice. In which order to use different tools in CLC Genome Finishing Module?

Clc genomics workbench assembly