HISAT-genotype is a next-generation genomic analysis software platform. Recent rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome upon which our genomic analysis has been based is substantially limited since it is a linear sequence or representation of only a few individuals. HISAT-genotype is based on a novel method, HISAT2, for representing and searching a significantly expanded model of the human reference genome using a graph, in which a comprehensive catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This new way of representing a population of genomes, along with a very fast and memory-efficient search capability, enables more detailed and accurate variant analyses than previous methods.
The initial version of HISAT-genotype includes a demonstration of its superior performance through HLA typing and assembly, a critical task in human organ transplantation. Because HISAT-genotype works well for these highly diverse genes, HLA genes, we anticipate it would be relatively straightforward to extend it to many, perhaps all, known variants in human genes. Based on the HLA genes and other well-studied genes soon to be included in HISAT-genotype, we will provide templates that researchers who have domain knowledge and expertise can easily use to input their own custom genotyping routines into our platform. This website is an online collaborative hub to encourage researchers around the globe to work together in developing the platform. Instead of genotyping one gene at a time, by researchers collaborating this platform will eventually be capable of analyzing an individual human genome with its over 20,000 genes within just a few hours on a personal computer, thus contributing to the advancement of personalized medicine.
- HISAT-genotype 1.0.0-beta release 6/8/2017 (first release)
- HISAT-genotype currently supports HLA typing, discovery of novel HLA alleles, DNA fingerprinting analysis, and CYP2D6 typing.
- The platform is currently designed for processing whole genome sequencing reads produced by Illumina platforms (e.g. 100 to 300 bps) and works great with paired-end reads and at least 20x coverage.
- We plan to create consortia to work together in enabling the platform to analyze the whole human genome with its >20,000 genes.