The sequencing read

Gencove - May 12, 2022

Introducing InfiniSEEK - Low-pass Genotyping Plus Target Capture in One Assay

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.

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Gencove - May 12, 2022

Gencove and NEOGEN® Launch InfiniSEEK™ — The First Whole Genome and Genotyping Sequencing Solution for Cattle Breeders

NEW YORK, N.Y., and LINCOLN, Neb., May 12, 2022 – Gencove, the leading low-pass whole genome sequencing and analysis software company along with NEOGEN® Corporation (NASDAQ: NEOG) today announced the launch of InfiniSEEK™, a revolutionary, cost-effective solution for whole genome sequencing and targeted SNP analysis from two trusted leaders in genomics.

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Gencove - Apr 28, 2022

Using a Modern Approach to Genotyping to Challenge Breed Stereotypes in Dogs

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.

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Kristi Ashton - Apr 13, 2022

TMG Selects Gencove’s Low-pass Whole Genome Sequencing and Analysis Platform as Part of Major Genomic Research and Development Initiative

NEW YORK, NY and Cambé, Brazil. – April 13, 2022 /GLOBENewswire/ – Gencove, the leading low-pass whole genome sequencing (LP-WGS) company and Tropical Improvement & Genetics (TMG), Brazil’s plant genomics company, today announced that TMG will be using Gencove’s LP-WGS platform to study soybeans as part of research and development investment.

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Miguel Liezun - Oct 27, 2021

Importing samples from Amazon S3

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.

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Gencove - Oct 26, 2021

Gencove Raises $10 Million to Meet the Global Demand for Accessible and Interpretable Whole Genome Sequencing at Scale

The company’s low-pass genome sequencing and bioinformatics platform provides a new way to power complete, accurate, and affordable genomic discovery

NEW YORK, NY — October 26, 2021 /PRNewswire/– Gencove, the leading low-pass genome sequencing platform company, today announced the successful close of a $10 million Series A investment bringing the company’s total financing to $16.2 million. The round was led by Lewis & Clark AgriFood with participation from new and existing investors including Spero Ventures, Techammer, Third Kind Venture Capital, and Version One Ventures. Funding will be used for further product development, commercial growth and to build out key business functions.

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Tomaz Berisa - Jul 4, 2021

Project-level permissions

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.

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Joe Pickrell, Data Scientist at Gencove - May 20, 2021

The coming commoditization of genome sequencing

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.

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Jeremy Li, Data Scientist at Gencove - March 16, 2021

New imputation pipeline using newly resequenced data from 3202 individuals

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.

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Jeremy Li, Data Scientist at Gencove - March 11, 2021

New publication in collaboration with the USDA: "Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers"

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.

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Jeremy Li, Data Scientist at Gencov - Mar 3, 2021

Gencove’s new pig haplotype reference panel

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.

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Jesse Hoff - Jan 29, 2021

Gencove’s improved cattle low-pass sequencing solution

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.

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Joe Pickrella - Jan 8, 2021

Enabling high-throughput SARS-CoV-2 sequencing and surveillance

At Gencove, our mission is to make genome sequencing accessible and interpretable. Over the past several weeks, it has become clear that a key missing piece of the response to the coronavirus crisis in the United States involves sequencing to monitor virus strains as they arise and spread. This was driven home by the identification of an apparently more contagious virus lineage in the UK and a potentially similar report from South Africa.

It seems certain that virus lineages with worrying properties (e.g. increased transmission or vaccine escape) are arising elsewhere in the world; these variants were only identified in the countries in question because they have systems for systematic viral surveillance by genome sequencing.

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Tomaz Berisa - Oct 22, 2020

Sample metadata

Users can now assign arbitrary JSON-formatted metadata to Gencove samples for downstream use.

We’ve been receiving consistent feedback from users saying they would like to store additional non-genomic data together with genomic data for their Gencove samples. These requests can be grouped into two broad clusters according to the nature of the data being stored:

  • Phenotypic data about the individual represented by the sample
  • Technical processing data
    • Batch information
    • Alternative or auxiliary identifiers

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