sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping | Zendy

Chia-Hua Chang | Zendy; Min-Te Chou | Zendy; Yi-Chung Wu | Zendy; Ting-Wei Hong | Zendy; Yun-Lung Li | Zendy; ChiaHsiang Yang | Zendy; JuiHung Hung | Zendy

Open Access

sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping

Author(s) -

Chia-Hua Chang,

Min-Te Chou,

Yi-Chung Wu,

Ting-Wei Hong,

Yun-Lung Li,

ChiaHsiang Yang,

JuiHung Hung

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw419

Subject(s) - acceleration , sequence (biology) , computer science , hardware acceleration , parallel computing , software , computer hardware , algorithm , arithmetic , computational science , computer graphics (images) , operating system , mathematics , physics , classical mechanics , biology , genetics

The Full-text index in Minute space (FM-index) derived from the Burrows-Wheeler transform (BWT) is broadly used for fast string matching in large genomes or a huge set of sequencing reads. Several graphic processing unit (GPU) accelerated aligners based on the FM-index have been proposed recently; however, the construction of the index is still handled by central processing unit (CPU), only parallelized in data level (e.g. by performing blockwise suffix sorting in GPU), or not scalable for large genomes.

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