US 11,810,648 B2
Systems and methods for adaptive local alignment for graph genomes
Kaushik Ghose, Malden, MA (US); and Wan-Ping Lee, Somerville, MA (US)
Assigned to Seven Bridges Genomics Inc., Charlestown, MA (US)
Filed by Seven Bridges Genomics Inc., Charlestown, MA (US)
Filed on Oct. 24, 2019, as Appl. No. 16/663,243.
Application 16/663,243 is a continuation of application No. 14/990,323, filed on Jan. 7, 2016, abandoned.
Prior Publication US 2020/0058374 A1, Feb. 20, 2020
Int. Cl. G01N 33/48 (2006.01); G01N 33/50 (2006.01); G16B 30/10 (2019.01); G16B 30/00 (2019.01)
CPC G16B 30/10 (2019.02) [G16B 30/00 (2019.02)] 19 Claims
OG exemplary drawing
 
1. A method, comprising:
using at least one hardware processor to perform:
accessing data indicative of:
a sequence read including genetic information; and
a graph representing a reference genome and variation in the reference genome,
the graph comprising nodes representing genetic sequences and edges connecting at least some of the nodes;
identifying a first portion of the graph including a first candidate mapping position;
selecting, from among multiple alignment algorithms and based on a measure of complexity of the first portion of the graph, an alignment algorithm to use for aligning the sequence read to the first portion of the graph, the multiple alignment algorithms including a first alignment algorithm and a second alignment algorithm different from the first alignment algorithm, the selecting comprising:
determining a number of paths through the first portion of the graph or a number of nodes in the first portion of the graph,
selecting the first alignment algorithm as the alignment algorithm to use for aligning the sequence read to the first portion of the graph, when either the number of paths through the first portion of the graph is greater than a threshold number of paths or when the number of nodes is greater than a threshold number of nodes, and
selecting the second alignment algorithm as the alignment algorithm to use for aligning the sequence read to the first portion of the graph, when either the number of paths through the first portion of the graph is less than or equal to the threshold number of paths or when the number of nodes is less than or equal to the threshold number of nodes; and
aligning the sequence read to the first portion of the graph using the selected alignment algorithm.