Blog

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.

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

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.

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.

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.

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

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.

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!