Welcome to the 10x Blog

From tips and tricks to 10x news, our blog is here to help you learn about all things 10x. Let us know what topics you would like to see in the Community Suggestions forum.

The extensive collection of Illumina sequencing datasets, described by Bo Zhou and his co-authors (Alexander Urban Lab, Depts. of Psychiatry and Genetics) in a recent bioRxiv preprint, are derived from J. Craig Venter’s genome.
Our fourth North American UGM of 2018 was held on May 18th in New York, and we’re happy to report that it was packed, both with information and attendees! 
The second European User Group meeting for 2018 took place in Uppsala, Sweden at the SciLife Lab. Over two days we saw many great talks from both 10x staff giving software demos and customers sharing their success stories.
Our 3rd North American User Group Meeting of the year took place on Thursday, April 26th, in Chicago, and we were thrilled to see so many members of the 10x community there!
In celebration of Earth Day this year, our own Andrew Gottscho, a conservation biologist and software field operations engineer, reports about his own experiences with endangered animals and the importance of genomics to study and help conserve these populations.
From posters to talks to our Exhibitor Spotlight co-sponsored with Miltentyi Biotec Day 2 at AACR 2018 was all about single cell genomics!
Today was a big day for 10x at AACR 2018! Not only did I get to check out a bunch of great posters and talks featuring 10x technology, but I also got to attend the 10x Genomics Workshop, “Revealing the True Biology of Cancer."
Our second UGM of 2018 was held on March 14th in South San Francisco, where we were joined by more than 150 customers and researchers from throughout the Bay Area.
It’s User Group Meeting season; catch up on what happened in San Diego
Linked-Reads and the Supernova Assembler enable low-cost, everyday diploid de novo assemblies. In this workshop 10x-perts David Jaffe and Nikka Keivanfar discussed Supernova assembly performance across a range of species, including human, insect, plant and vertebrates, and highlighted improvements to our high molecular weight DNA sample preparation protocols, including a new protocol for single insects.
We were recently able to sit down and catch up with Hagen Tilgner about his team’s new manuscript that provides a more comprehensive understanding of the human transcriptome, “Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome”, published in Genome Research.
In a recent Nature Communications publication, Hammond et al., report on sequencing, assembly and annotation of the draft North American bullfrog genome.
In a recent publication in Nature Communications, Porubsky, et al. combined strand-specific single-cell sequencing (Strand-seq) with long-read or Linked-Read sequencing to introduce an integrative method for phasing individual human genomes.
Researchers recently introduced a new software package for simulating Linked-Reads call LRSim. In a new paper by Luo et al., the authors demonstrate how the software can be used to optimize Linked-Read sequencing results.
The 2017 Australasian Genomic Technologies Association (AGTA) in Hobart, Tasmania wrapped up last week and a common theme of the meeting was both applications and technical challenges of single-cell analysis.
In a recent Bioinformatics publication, researchers presented ARCS, a new application that uses 10x Linked-Reads to further organize draft genomes into highly contiguous assemblies.
The American Society of Human Genetics (ASHG) annual meeting continued in Orlando, FL and Thursday bought our 10x Software workshop "Intuitive Tools for Sequence Analysis: Crunching Genomic, Single-Cell, and Immune Repertoire Data Using 10x Chromium™ Software” and an exciting PerkinElmer workshop where they discussed "Linked-Reads: Enabling Robust Genome Analysis from Dried Blood Spots”.
Linked-Reads provide long-range information enabling structural variant detection and phasing of genome and exome sequencing data.  In our third 10x-pert Workshop session, our R&D 10x-perts provided an overview of the Loupe™ Genome Browser for structural variant detection and took closer look at visualizing simple structural variants and deriving complex events.
Have you ever wondered how to best prepare your samples or how much sequencing you need to achieve the highest quality Linked-Read data? We recently published a Bench Tips article with Biocompare, where we highlight important tips to make the most of our Linked-Read technology for long-range genomic analysis.
Researchers at Stanford University have developed novel bioinformatics tools that leverage 10x Genomics’ Linked-Read sequencing to phase and resolve the complete structure of cancer genomic rearrangements. 
Two recent publications applied the power of Linked-Reads and the Chromium™ Genome Solution to genetically characterize gastric and triple-negative breast cancer. In both cases, the researchers discovered complex genomic rearrangements that they associated with the amplification of oncogenic driver genes.
Get the most out of your Linked-Read data with Long Ranger™ version 2.1.4: improved run-times, extended support for NovaSeq and more.
There are many examples of how microbes influence the behavior of animals; however, studying the molecular basis for microbial behavior manipulation has suffered from a lack of tools. At our Bay Area User Group Meeting, Carolyn Elya spoke about establishing a D. melanogaster – E. muscae system and setting out to sequence and assemble the mind-controlling fungal pathogen.
Using 10x Linked-Read technology combined with standard, short-read sequencing, Dr. Noah Spies and his team at Stanford University were able to develop a statistical method for complex structural variant detection—Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs).
The Supernova™ Assembler enables true diploid assembly from Linked-Reads and the latest release makes everyday de novo assembly more accessible than ever.
Genomic analysis is an important tool for conservation biology, enabling researchers to help better understand and preserve endangered species. In a new Biorxiv preprint, researchers at Johns Hopkins describe a cost-effective and low DNA input method of de novo assembly for the endangered Hawaiian monk seal genome using 10x Linked-Reads and Supernova™ software.
Although thousands of human genomes have been sequenced in the last decade, de novo assembly of individual genomes is not common due to the high cost and experimental burden.  In a recent Genome Research paper, Weisenfeld et al describe a straightforward, low cost method for creating true diploid de novo assemblies using 10x Genomics Linked-Reads and the Supernova™ assembler.
The large scale and repetitive nature of conifer genomes make them an important benchmark for assembly technologies. At 31 Gb, the Pinus lambertiana (sugar pine) genome is the largest genome assembled to date. Using the GemCode™ System from 10x Genomics, researchers at UC Davis scaffolded the de novo assembly and produced a new reference assembly for sugar pine with 8-fold improvement in contiguity.
In a recent publication from the Broad Institute of MIT and Harvard, researchers identified >11,000 distinct structural variations among participants with autism spectrum disorder. These results provide new insights into the extent and diversity of structural variation present in the morbid human genome.
The InPSYght schizophrenia and bipolar disorder sequencing project seeks to produce Whole Genome Sequencing (WGS) data to identify variants associated with disease, build a reference panel of structural events and haplotypes to impute into large genotype data sets, and create and share data and methods with the community.