Huawei Technologies Co., Limited

Meysam Roodi

Zahra Lak

In accordance with embodiments, a processing unit performs alignment of a short read (SR) against a reference sequence. The reference sequence comprises a first sequence of base pairs (bps). The SR comprises a second sequence of bps. The processing unit determines whether the SR is aligned. If the SR is not aligned, the processing unit receives the next SR and processes the next SR by repeating. If the SR is aligned, in response to the determination that the SR is aligned with the reference sequence at a first position in the reference sequence, the processing unit generates an SR metadata entry corresponding to the SR. The processing unit inserts the SR metadata entry to a linked list in a SR metadata collection. The position of the linked list in the SR metadata collection corresponds to the first position of the reference sequence where the SR is aligned.

Merging alignment and sorting to optimize computer operations for gene sequencing pipeline

In accordance with embodiments, 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.

Memory allocation to optimize computer operations of seeding for burrows wheeler alignment

In accordance with embodiments, a computing device of a processing system performs a seed search of a short read (SR) against a reference sequence using a Burrows Wheeler Transform (BWT) algorithm to determine a seed. During the seed search one or more seed candidates in the reference sequence are determined. If the number of matches is less than or equal to a predefined threshold value the seed search using the BWT algorithm is stopped. Each seed candidate is extended to a respective extended seed candidate equal in length to the SR. bp-to-bp comparisons are performed between a remaining bp sequence of the SR after the matching bp and a corresponding remaining bp sequence in each extended seed candidate. An extended seed candidate that exactly matches the SR in the bp-to-bp comparisons is outputted as the seed.

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Richmond Hill, Canada

Meysam Roodi