de novo Assembly Solution

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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.

Our 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*
View the Workflow

*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.


The 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′, V(D)J, Genome and Exome Solutions. A dedicated Chromium Single Cell Controller is also available for users that exclusively run our Chromium Single Cell 3′ and V(D)J Solutions.

View Our Controller Gallery


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
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HMW DNA sample preparation techniques and best practices

Jill Herschleb, PhD
10x Genomics
November 28, 2017
Pleasanton, CA

Structural variant and haplotype analysis with Linked-Read data

Sarah Garcia, PhD & David Stafford
10x Genomics
November 28, 2017
Pleasanton, CA

Genome assembly of the mind-controlling fly pathogen E. muscae via 10x Genomics

Carolyn Elya
University of California, Berkeley
March 21, 2017
User Group Meeting – San Francisco, CA

De novo assembly of a large size genome: the olive fruit fly

Jiannis Ragoussis
McGill University
February 13, 2017
AGBT Annual Meeting – Hollywood, FL

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
*Pre-prints are available at BioRxiv.

Assembly of individual chromosomes at megabase scale using 10x Linked-Reads

  • Genome Informatics
    Cold Spring Harbor Laboratory, New York
    November 1 – November 4, 2017

Direct determination of genome sequences

  • Wellcome Trust Genome Informatics Conference
    Cambridge, UK
    September 19 – 22, 2016
  • The Biology of Genomes
    Cold Spring Harbor, NY
    May 10 – 14, 2016

Order your Chromium Controller, today.

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