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Microbial Genome Finishing Module
CLC Microbial Genome Finishing Module is designed for finishing of bacterial genomes or genomes of similar size. The module contains a range of tools designed to automate steps in the finishing process, help organise contigs and solve problems in assemblies. The module is an add-on to CLC Genomics Workbench.
High-throughput sequencing technologies enable rapid full-genome sequencing of genomes. However, short read lengths and repetitive sequences often complicate full genome assembly and result in fragmented assemblies. The Genome Finishing Module includes a variety of different tools with different functionalities that can be used to find, visualize and solve problems in genome sequences.
Key tools in the module
| Align Contigs | Aligns contigs to a reference sequence or, in the absence of a reference, to the contigs themselves. Also provides a platform to easily visualize and edit contigs |
| Analyze Contigs | Analyzes the contig read mappings for possible misassemblies, single strandedness, coverage, broken pairs, and unaligned ends |
| Create Primers | Automated primer design for re-sequencing purposes |
| Find Sequence | Tool to search for names, sequences or annotations in sequencing data |
| Collect Paired Reads Statistics | Detects paired reads that map to separate contigs and estimates the distance between the contigs and the relative orientation of these |
| Reassemble Regions | Targeted reassembly of contig regions for solving small misassemblies |
Tutorial: Using the Align Contigs tool
The Genome Finishing Module is a collection of tools that has been developed to help finish microbial genomes. This tutorial is an introduction to the Align Contigs tool, one of the most important tools in the Genome Finishing Module toolbox that can be used to easily visualize and edit contigs.
In brief, the purpose of the Align Contigs tool is to use a reference sequence to direct the order and orientation of the individual contigs by aligning the contigs to the reference sequence. If no reference sequence is available, the contigs may be aligned against themselves in order to identify potential overlapping contigs that could be joined.
Read the full tutorial
