The Chromium™ De Novo Assembly Solution

True Diploid Assembly with the Supernova™ Assembler

Discover the true genome with the Supernova Assembler and open the door to low-cost, everyday diploid assemblies. Unlock sample-specific sequences, probe diploid genome structure and remove the need for a reference sequence of any kind.

The 10X De Novo Assembly Solution Features:

  • True diploid assembly unlike other methods
  • Fast and simple de novo assembly workflow
  • Go from sample to assembly in <2 weeks
  • 10 Mb scaffold size and long range accuracy
  • High-quality assembly from as little as 1 ng of DNA
  • Validated and supported for human genomes*

*Note on non-human samples: Supernova™ is a de novo assembly program that has been designed to assemble germline human genomes, from data generated using Chromium™ Genome Reagent Kits. 10x Genomics has validated Chromium™ Genome Reagent Kits and Supernova only on human genomes. Therefore, using Supernova to assemble non-human genomes is experimental and may have unexpected features that limit assembly quality. Despite this, many users have successfully assembled non-human genomes using Supernova.

page-single-cell-controller-pictureThe Chromium™ Controller

Compact, sleek, efficient.

The compact, sleek Chromium™ Controller has been designed to rapidly and efficiently automate the equivalent of 100,000s to 1,000,000s of pipetting steps for highly parallel sample partitioning and molecular barcoding. The Chromium Controller allows a user to run any of our Chromium Single Cell 3′, Genome and Exome Solutions. A dedicated Chromium Single Cell Controller is also available for users that exclusively run our Chromium Single Cell 3′ Solution.


Chromium Genome v2 Library Kit & Gel Bead Kit

The Chromium Controller now supports our new Chromium Genome Reagent Kits with v2 chemistry, with the following refinements:

  • Chromium Genome Library Kit & Gel Bead Kit v2 comes in 16 and 96-reaction (HT) configurations, offering a flexible workflow that can be scaled based on the needs of each user
  • The Chromium Genome HT Library Kit & Gel Bead Kit v2 can be automated on industry standard liquid handlers and has a significant cost advantage per sample


  • Chromium Genome HT Library Kit & Gel Bead Kit v2, 96-reactions
  • Chromium Genome Library Kit & Gel Bead Kit v2, 16-reactions
  • Chromium Genome Chip Kit v2, 48-reactions

Purchase Separately:

  • Chromium i7 Multiplex Kit, 96-reactions


The Chromium™ de novo Assembly Software Suite

Supernova™ Assembler is a software package for de novo assembly from Chromium Linked-Reads.

The Supernova™ Assembler software package includes:

  • supernova mkfastq
  • supernova run
  • supernova mkoutput


Scientific Seminars

Everyday de novo assembly with the Supernova Assembler

David Jaffe
10x Genomics, Inc.
September 10, 2016
Pleasanton, CA

Improving genome analysis with Linked-Reads

Deanna Church
10x Genomics, Inc.
August 15, 2016
Pleasanton, CA


ARCS: Assembly roundup by Chromium scaffolding

Yeo S et al. 2017 Jan 17; Pre-print*.

De novo assembly and phasing of a Korean human genome

Seo JS et al. Nature. 2016 Oct 5;538(7624):243-247. doi: 10.1038/nature20098. PMID: 27706134.

Assembly of the complete Sitka Spruce chloroplast genome using 10x Genomics’ GemCode sequencing data

Coombe L et al. PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. PMID: 27632164.

Direct determination of diploid genome sequences

Weisenfeld NI et al. 2016 Aug 19; Pre-print*.

ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter

Jackman SD et al. 2016 Aug 7; Pre-print*.

A hybrid approach for de novo human genome sequence assembly and phasing

Mostovoy Y et al. Nat Methods. 2016 Jul;13(7):587-90. doi: 10.1038/nmeth.3865. PMID: 27159086.

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