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.

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.
Elfin, Aurora and Qila leave their mark — Reference-Quality genome assemblies for the Northern Sea Otter and Beluga Whale inform conservation efforts and health studies
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.
In celebration of their upcoming 25th anniversary, The WellcomeTrust Sanger Institute will be collaborating with a number of leaders in the genomics field, including 10x Genomics, on their 25 Genomes Project, an exciting effort to comprehensively sequence 25 new genomes of species found in the UK.
In a recent Nature Communications publication, Hammond et al., report on sequencing, assembly and annotation of the draft North American bullfrog genome.
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.
High quality high molecular weight (HMW) DNA is key to getting the most out of Linked-Read data. In a recent 10x-pert Workshop session, our R&D 10x-pert discussed general tips and best practices for isolating HMW DNA and took a closer look at two of our demonstrated protocols for HMW DNA isolation from fresh frozen tissues and DNA size selection.
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.
The Supernova™ Assembler enables true diploid assembly from Linked-Reads and the latest release makes everyday de novo assembly more accessible than ever.
There’s a growing number of data analysis tools being developed for single cell and Linked-Read applications, including gene expression, genome assembly, structural variant detection and more.  Check out the list we’ve compiled so far.
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 recently published paper, entitled “Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data” researchers used GemCode’s novel Linked-Read data type for de novo assembly of a complete chloroplast genome.
Linked-Reads provide the long range information missing from standard short read sequencing approaches, enabling reconstruction of long range haplotypes, detection of complex structural variants and the ability to perform de novo genome assembly.