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CLC Genome Finishing Module

A fast track to the finishing line.

Short read lengths and repetitive genomic regions often result in fragmented de novo assemblies.To improve assembly quality and convert contigs into high quality assemblies a complex process referred to as Genome Finishing needed. Unfortunately genome finishing is work-intensive and time-consuming and often involves expert teams.

CLC Genome Finishing Module is an add-on to CLC Genomics Workbench, designed to accelerate and simplify genome finishing, and make this process accessible to life scientist without deep understanding of bioinformatics.

Towards high quality reference genomes

Automation where possible
The module automates steps like scaffolding, contig joining, and the ordering of contigs relative to each other or a closely related reference genome.

Manual editing where necessary
Automated steps improve the outcome of the initial assembly. Visually inspect and improve the remaining unresolved regions with the help of manual editing tools like the Analyze Contigs tool.

Back to the bench
If it is necessary to amplify and resequence regions between contigs, CLC Genome Finishing Module identifies useful primer combinations for you.Once new amplicon data are available they can be readily used to improve an assembly.

Scale up your analysis
Need for high-performance computing? With the Genome Finishing Server Extensions you can extend the features of the module to your CLC Genomics Server.

Full list of features included here

Improving assembly quality made fast and easy

Use the join contigs tool and leverage in one step a combination of finishing methods like scaffolding using paired reads or long read (like PacBio) data, or automatic alignment of contigs to each other or to a closely related genome.

Utility for most commonly sequenced genome types
The module was designed for finishing smaller genomes, and is ideal for assembling microbes, eukaryotic parasites, or fungi. Automated tools for scaffolding or contig joining also improve results for larger genome assemblies, but manual editing is not feasible for plant or animal genomes.

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Tutorials

As an introduction to the module tools we have some videos and PDF tutorials guiding your way through different aspects of the genome finishing.

Screenshots

The Looks

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