Jeremy Li, Director of Data Science - Sep 25, 2023

A deep dive into Explorer analysis cloud

At Gencove, we have repeatedly seen the complexity and insufficiency of existing tools limit research teams from fully unlocking the value of their genetic data. Gencove Explorer analysis cloud represents a full-stack solution that addresses the challenges that exist with currently data solutions, in a single integrated platform and with a minimal learning curve. In doing so, Explorer accelerates the rate at which scientists can answer critical biological questions, and furthers our goal of delivering insights that advance global health and sustainability.

Read More >

Lex Flagel, Staff Data Scientist - Sep 19, 2023

An updated evaluation of a recent open-access human genome reference panel for low-pass imputation

The Broad recently released an update to the HGDP1KG panel as part of the gnomAD_v3.1.2 release that included several tweaks and changes meant to increase the accuracy of the combined panel. In this blog post we once compare imputation performance of this updated panel to the NYGC1KG panel.

Read More >

Jeremy Li, Director of Data Science - Sep 08, 2023

Improving biological sample and data management with sample manifests

The new "sample manifests" feature ensures accurate sample identification and reduces errors, streamlining the process from sample collection to solutions delivered by the platform.

Read More >

Jeremy Li, Director of Data Science - Aug 15, 2023

Investigating the impact of reference panel errors on imputation quality and genotype accuracy

Genotype imputation is an increasingly popular method used in population scale genomic studies that relies on two key elements; the haplotype reference panel (HRP) and the imputation algorithm. A recent preprint from the Gencove data science team dives into how common errors in reference panels impact imputation accuracy and the interplay between the two across a spectrum of sequencing coverages.

Read More >

Gencove Team - Aug 10, 2023

Low-pass sequencing and imputation for evaluating genetic variation

Low-pass whole genome sequencing is an approach that strikes a balance between the cost-efficiency of microarrays and the broad genomics insights provided by high coverage WGS

Read More >

Jeremy Li, Director of Data Science - Jul 26, 2023

Gencove platform update offers phased genotypes, improved imputation of sex chromosomes and faster processing times

Staying at the cutting-edge of the latest bioinformatic tooling is critical to navigating the dynamic landscape of genomics. We are pleased to announce several new optimizations and improvements to our standard pipeline offerings that will reduce processing time and resources.

Read More >

Jesse Hoff, Agrigenomics Product Manager - Jul 10, 2023

Exploring the power of low-pass WGS with target capture in plant breeding

Gencove and Twist Biosciences have partnered to pressure test the utility of lp-WGS plus target capture and imputation for a major crop species, soybeans, demonstrating that lp-WGS with target capture works well in plants and covers a large panel.

Read More >

Forest Dussault, Software Engineer - Jun 22, 2023

Introducing a new way to bring FASTQ files to the Gencove platform

We’re excited to announce that we are introducing a new feature that will make bringing users’ FASTQ files onto Gencove’s platform easier than ever.

Read More >

Oliver Arnstein, Software Engineer - Jun 15, 2023

Increasing insight into subscription notification history

We're pleased to announce a new feature on Gencove's web interface that now allows users to see a detailed list of notifications sent by a subscription

Read More >

Jeremy Li - Mar 23, 2023

An evaluation of imputation accuracy in a recently released open-access genomic dataset using low-pass sequencing

In this blog post, we describe some imputation performance benchmarks for a recently released haplotype reference panel from the Martin Lab comprising haplotypes from high-depth sequence data from the 1000 Genomes project and the Human Genome Diversity Project and compare them against corresponding benchmarks for the New York Genome Center's resequencing effort of the 1000 Genomes project.

Read More >

Angie Mosquera, Software Engineer - Mar 21, 2023

User-customizable project configurations

We are pleased to announce a new feature that allows users to customize project configurations on the Gencove platform and provides our users with greater control over their projects.

Read More >

Mamad Ahangari, Data Scientist - Mar 13, 2023

Low pass sequencing plus imputation in cattle outperforms imputation from genotyping arrays

Over the past decade, the cost of genome sequencing has significantly decreased, leading to a rise in popularity of alternative sequencing methods such as low-pass whole genome sequencing instead of genotyping arrays. To meet this demand, at Gencove, we offer a cost-effective solution for generating genome-wide information by providing low-pass whole genome sequencing plus imputation as a high-throughput alternative to genotyping arrays. Our previous research has already established that low-pass whole genome sequencing outperforms traditional genotyping arrays in terms of imputation in humans (Li et al., 2021). In this blog post, we describe the results of a recent experiment where we demonstrate that imputation using low-pass whole genome sequencing is also superior to genotyping arrays in cattle.

Read More >