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The Simplot and Gencove genomic EPD provides a benchmark from which bulls can be evaluated for cardiac morphology significantly reducing their calves’ morbidity and mortality and increasing their overall economic performance.

To offer another option for scientists and companies seeking whole genome sequencing and analysis, Gencove evaluated the ability to process low-pass sequencing data derived from the AVITI™ System in two studies.

Whether it is genotyping a whole herd or building support for new species and breeds, at Gencove, we’re continually looking for ways to empower companies and scientists to discover more using sequencing. That’s why we’re excited to share the latest milestone in this pursuit with the launch of InfiniSEEK™– available now through NEOGEN.

Do you rate your golden retrievers high on the scale for friendliness to strangers because they’ve been bred to demonstrate that trait or because you house an internal bias that tells you golden retrievers are friendly? These are precisely the types of questions that researchers are answering by utilizing modern, genome-wide sequencing information to better understand the association between genes and traits in dogs.

The vision of Gencove is that the universal application of genomics will result in a healthier and more sustainable civilization.

At Gencove, we are committed to making genome sequencing more accessible. To that end, we are pleased to announce the ability to use Amazon S3 directly as an import origin in addition to supporting uploads through our CLI, our API, or from BaseSpace. The new feature saves time because samples can now be imported directly from an S3 bucket without the need to download and then upload again. In this post, we show how to import samples from a S3 URI to a project.

tl;dr: users’ permissions can now be escalated on a per-project basis and auditing user access has become easier.

We’ve recently released an upgrade to Gencove’s permission system, which enables escalating permissions on a per-project basis. This is done by specifying a project-specific role in addition to the user’s organization role and can be done separately for each project in the organization.

For example, in a situation where the organization would like users to have view access to only a subset of projects, users with the Owner role in the organization would invite others to join the organization with the Member or Uploader role and assign project-specific Viewer roles as needed.

tl;dr: new competition in genome sequencing hardware will drive expanded use cases for sequencing analytics across industries

In Nature’s Metropolis, the brilliant economic history of Chicago, William Cronon describes the shifts in power between agricultural producers and different industrial groups as technologies like the grain elevator upended traditional market relationships.

In this telling, a set of small steps gradually severed the connection between the buyer of a grain like corn and its original source — while in 1850 someone might buy a bag of corn from an individual producer and know that each individual kernel came from a specific plot of land, by 1880 that same buyer would likely be buying a quantity of "Number 2", pooled from corn produced in any number of anonymous locations.

The 1000 Genomes Project was completed in 2015 and culminated in its "phase 3 release" of phased genotypes from 2504 individuals at over 80 million variants, and remains the largest fully open-sourced genomic dataset [0]. The final variant callset was based on a combination low-coverage whole-genome sequencing (at an average of around 7x) along with whole exome sequencing and results from genotyping array assays of these individuals.

Along with Warren Snelling and other colleagues at the USDA MARC (Meat Animal Research Center), we recently performed a study investigating the utility of imputation from low pass sequencing data in cattle in the context of genomic prediction for beef steers. This study is now published in MDPI Genes and can be accessed at the following link [0]. In this blog post, we briefly review the motivations behind this study and outline the main results.

At Gencove, we’re continuously expanding the selection of species which can be used with imputation pipelines based off of low-pass sequencing. Unlike, for instance, cattle in the form of the 1000 Bull Genomes Project [1], there does not currently exist a large-scale public resequencing effort to characterize the genetic diversity of extant breeds used for agricultural purposes, and the existing literature on the performance on genotype imputation in pigs is primarily limited to genotyping array imputation [2,3,4].

To address this current shortcoming, we have recently developed and released a pipeline for low-pass sequencing in pigs on the latest reference genome (Sscrofa11.1/susScr11) and a diverse haplotype reference panel encompassing the range of genetic diversity in the most common breeds found in the swine industry.

The new product supports more breeds and returns higher accuracy through an updated reference panel. We have also made it easier to use for industrial scale applications.

We are excited to announce an update to our cattle imputation reference panel, which now includes over 50 breeds and 1800 animals. This better supports the demand we’ve had for all the most important breeds being utilized by the cattle industry today. Since launching our original panel, we’ve been busy optimizing our pipeline and adding new features to make low-pass sequencing more powerful and easier to use. We believe this platform is now the best high-throughput solution for building genomic breeding programs.