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10x Genomics
Chromium De Novo Assembly

Overview of De Novo Assembly Software

Before generating Supernova data, please carefully read Achieving Success with De Novo Assembly. Please also review Supernova performance on twenty human and nonhuman datasets.

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes.

The Supernova software package includes two processing pipelines and one for post-processing:

How to cite Supernova

Please refer to our 2017 paper "Direct determination of diploid genome sequences" for broad algorithmic details and assessment of computational performance and assembly quality for Supernova 1.2. There have been changes to algorithms and results since then.

For the Linked-Read laboratory technology that Supernova exploits, please refer to