Compressively-accelerated read mapping framework for next-generation sequencing
US10230390B2 · kind B2 · utility
Inventors
Key dates
| Filing date | Aug 27, 2015 |
| Grant date | Mar 12, 2019 |
| Priority date | — |
| Expiry date | Feb 24, 2036 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG16B50/50
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.