Title:
METHOD AND SYSTEM FOR MEMORY ALLOCATION TO OPTIMIZE COMPUTER OPERATIONS OF SEEDING FOR BURROWS WHEELER ALIGNMENT
Document Type and Number:
WIPO Patent Application WO/2020/182172
Kind Code:
A1
Abstract:
A processing unit receives a count table and an occurrence table for a reference sequence generated using a Burrows Wheeler Transform (BWT) algorithm. The reference sequence comprises a sequence of base pairs (bps). The processing unit stores a first part of the occurrence table in a first type of memory. The size of the first part of the occurrence table is determined based on a size of the first type of memory and a first number of bps of short reads (SRs) to be processed using the first type of memory. The processing unit receives a short read (SR) of a sample sequence. The SR comprises the first number of bps and a second number of bps. The processing unit performs alignment of the short read (SR) against the reference sequence using the count table and the occurrence table.
Inventors:
ROODI MEYSAM (CA)
LAK ZAHRA (CA)
LAK ZAHRA (CA)
Application Number:
PCT/CN2020/078900
Publication Date:
September 17, 2020
Filing Date:
March 12, 2020
Export Citation:
Assignee:
HUAWEI TECH CO LTD (CN)
International Classes:
G16B30/00
Foreign References:
| US20150363549A1 | 2015-12-17 | |||
| US20140163900A1 | 2014-06-12 | |||
| US20120330567A1 | 2012-12-27 | |||
| CN106687966A | 2017-05-17 |
Other References:
HENG LI , RICHARD DURBIN: "Fast and accurate short read alignment with Burrows–Wheeler transform", BIOINFORMATICS, vol. 25, no. 14, 15 July 2009 (2009-07-15), pages 1754 - 1760, XP055553969, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btp324
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