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THE CHROMIUM DE NOVO ASSEMBLY SOLUTION

HIGHLIGHTS

• Create true diploid assembly

• Fast, cost-effective and simple de novo assembly workflow

• Go from sample to assembly in as little as 1 week

• 10Mb scaffold size and long range accuracy for human assemblies

• High-quality assembly from as little as 1ng of DNA and HMW DNA fragments

• Eliminate reference bias in your genome sequence

HUMAN

PLANTANIMAL

Everyday de novo Assembly

THE CHROMIUM SYSTEM | DE NOVO ASSEMBLY | PRODUCT SHEET

Reconstruct diploid genomes

Scaffolding and phasing a diploid assembly

separate assemblies of homologous loci

The creation of a true diploid de novo assembly is critical to understanding the real nature of an individual genome in order to facilitate more personalized human disease research, understand the true diversity of individuals in population studies, and create accurate reference genomes for diploid organisms. By partioning and barcoding high molecular weight (HMW) DNA to generate Linked-Reads, long range contextual information of the genome can be derived from short-reads. Low-cost, everyday diploid assemblies are easily achieved by consolidating multiple assays into a single, powerful workflow with low sample input require-ments. Discover the true genome and unlock allele-specific sequences, probe diploid genome structure, and remove the need for a reference sequence of any kind with our Chromium de novo Assembly Solution.

The Supernova Assembler exploits Linked-Reads data to reconstruct a diploid genome, unlocking allelle- specific sequence and removing the need for a reference sequence of any kind.

High quality diploid genome sequences can be obtained through the assembly of Linked-Reads. The Superno-va Assembler is a collection of algorithms that construct and phase diploid assemblies.

© 2019 10X Genomics, Inc. FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.LIT000021 Rev C Chromium De Novo Assembly Product Sheet

Everyday de novo Assembly THE CHROMIUM DE NOVO ASSEMBLY SOLUTION

PRODUCTS PRODUCT CODE

Chromium Genome HT Library & Gel Bead Kit v2, 96 rxns1 120261

Chromium Genome Library Kit & Gel Bead Kit v2, 16 rxns1 120258

Chromium Genome Chip Kit v2, 48 rxns1 120257

Chromium i7 Multiplex Kit, 96 rxns 120262

Chromium Controller & Accessory Kit, 24 Mo. Warranty

120246

Chromium Controller & Accessory Kit, 12 Mo. Warranty

120223

The Supernova Assembler go.10xgenomics.com/assembly/supernova

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Sample Size (Gb) DNAsize (kb)N50

contig (kb)N50

scaffold (kb)HET SNP

spacing (kb)N50 phase block (Mb)

NA12878 3.2 95.5 85.0 12.8 1.7 2.8

NA24385 3.2 111.3 90.0 10.4 1.5 3.9

HGP 3.2 138.8 104.9 19.4 1.5 4.6

Yoruba 3.2 126.9 100.5 16.1 1.1 11.4

Komodo Dragon 1.8 85.4 95.3 10.2 10.3 0.4

Spotted owl 1.5 72.2 118.3 10.1 7.1 0.2

Hummingbird 1.0 86.2 87.6 12.5 0.4 10.1

Monk seal 2.6 92.3 93.8 14.8 17.7 0.6

FEATURED PUBLICATIONS

Weisenfeld NI et al. Direct determination of diploid genome sequences. Genome Res. 2017 May. doi: 10.1101/gr. 214874.116. PMID: 28381613.

Coombe L et al. Assembly of the complete Sitka Spruce chloro-plast genome using 10x Genomics’ GemCode sequencing data. PLoS One. 2016 Sep. doi: 10.1371/journal.pone.0163059. PMID: 27632164.

Yeo S et al. ARCS: Scaffolding genome drafts with Linked-Reads. Bioinformatics. 2017 Oct. doi: 10.1093/bioinformatics/btx675. PMID: 29069293

APPLICATIONS

• Reference Genome Creation• Hybrid de novo Assembly• Production Gene-Level de novo Assembly

Sample data from the Supernova Assembler

ADDITIONAL RESOURCES

LINKED-READS 10xgenomics.com/linked-reads

DATASETS go.10xgenomics.com/assembly/datasets

SEMINARS go.10xgenomics.com/assembly/seminars

APPLICATION NOTES go.10xgenomics.com/assembly/app-notes

TECHNICAL SUPPORT go.10xgenomics.com/assembly/support

PUBLICATIONS go.10xgenomics.com/assembly/pubs

RESEARCH AREA

• Agrigenomics• Inherited Disease• Cancer Genomics• Population Genetics• Biodiversity • Gene Editing

1 Available for use only with the indicated Chromium Controller (PN 120223 or 120246).

We tested the Supernova Assembler on four human samples and five non-human samples. Human samples included three standard cell lines and blood from a HGP (Human Genome Project)

donor. Non-human samples (provided by collaborators) included the Komodo dragon, spotted owl, hummingbird, and monk seal..