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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.

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.

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.

New pipeline available: salmon

Samples already on the Gencove platform can now be easily reprocessed using a different project configuration.

To help move towards Gencove’s vision of ubiquitous sequencing, we’re happy to announce support for our deep whole genome sequencing (WGS) pipeline!

Invest in a genotyping solution that changes with your breeding program. The Gencove platform ensures backward compatibility, adaptability to new markers and reference genomes, additional analyses, and continual innovation.

Improve molecular breeding efficiency with a modern genotyping approach that can be set up in a few weeks plus turns your samples around quickly!

Gencove’s low-pass sequencing platform is at cost-per-sample price parity with many microarray assays across a wide range of species in both plants and animals. That makes Gencove the best choice for getting the utility of sequencing data at microarray prices.

There’s no question that sequencing is a powerhouse of utility for genetics in breeding. However, does it meet the requirements to become a routine tool for genomic selection in breeding programs?

Pharmaceutical companies use Whole Exome Sequencing (WES) in their drug discovery and development process. However, R&D teams still need a comprehensive view of genomic variation outside the exome. Historically, the only way to augment WES was with arrays, but now pharma companies have an alternative - low-pass whole genome sequencing.