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CLC Genome Finishing Module

Fast track to the complete picture

Short read lengths and repetitive genomic regions often result in fragmented de novo assemblies. To improve results and convert contigs into high quality assemblies a complex process referred to as genome finishing is needed.

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

Genome finishing is usually work-intensive and time-consuming, and often involves specialized teams. CLC Genome Finishing Module puts non-experts on the fast track towards finished genome assemblies.

Automation where possible

The module automates steps like scaffolding, contig joining, and the ordering of contigs relative to each other or to a closely related reference genome. New for PacBio users: Easy and rapid error correction and assembly of PacBio data into gold-standard reference genomes.

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 high-performance computing? With the Genome Finishing Server Extension you can extend the features of the module to your CLC Genomics Server.

Improving assembly quality - fast and easy

Improve your de novo assembly using Join Contigs. Leverage in one step a combination of finishing methods. Scaffold contigs using paired reads or long read (like PacBio) data, and carry out automatic alignment of contigs to each other or to a closely related genome.

Assemble reference genomes faster. PacBio’s single molecule real-time sequencing platform generates data fast. Is data analysis now your bottleneck? We bring you the fastest and simplest way to error-correct and assemble PacBio long reads into high quality assemblies with CLC Genome Finishing Module.

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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We frequently release updates and improvements such as bug fixes, new features or plugins. To get a complete overview, please visit latest improvements.


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

PDF tutorial is available here
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