Gencove has developed a new low-coverage Whole Genome Sequencing (WGS) process to replace commonly used SNP Arrays. We sequence a random 10% to 20% of the genome in contrast to a SNP array, where about 0.02% of the genome is covered. Using a method called imputation, we can compare the sequenced bits to reference genomes and fill in many of the blanks.
The Gencove platform allows you to track every step of your research project and your participant activity. You also get immediate access to your resulting data in multiple formats.
What is the advantage of using an API instead of requesting a file upload?
User uploads can come from many different companies and in many different formats, and user errors mean that files are sometimes corrupted. User uploads also are not possible on mobile devices. We handle all of these issues, and standardize the genomic data using imputation. Once a user has their data on Gencove, it’s available to you whether the user reaches your site on desktop or mobile.
What data are available through the API?
The data you can request from a user include the original genotype/sequencing data (e.g. a sequencing BAM file or an ancestryDNA text file), an imputed VCF, an ancestry summary for the individual and (if applicable) a microbiome summary.
Can you help me build an app or website for phenotyping?
Yes, please contact us at firstname.lastname@example.org to discuss your project.
What is genotype imputation?
Genotype imputation is a method for using measured genetic variants to fill in the “missing” ones that have not been measured. It works because we know from thousands of sequenced genomes that there are set of genetic variants that are all found together, and so if you measure one of them you can guess with high probability to remainder. Learn more on Wikipedia.
What reference panel do you use for imputation?
We currently use the 1000 Genomes Phase 3 reference panel. We are experimenting with the Haplotype Reference Consortium data, if you have specific reference panel needs, please contact us at email@example.com.