GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Abstract Background Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pair...

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Bibliographic Details
Main Authors: Shanshan Ren, Nauman Ahmed, Koen Bertels, Zaid Al-Ars
Format: Article
Language:English
Published: BMC 2019-04-01
Series:BMC Genomics
Subjects:
Semi-global alignment with traceback
Optimal alignment
GATK HaplotypeCaller (HC)
GPUs
Online Access:http://link.springer.com/article/10.1186/s12864-019-5468-9

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http://link.springer.com/article/10.1186/s12864-019-5468-9

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