GANDAFL: Dataflow Acceleration for Short Read Alignment on NGS Data

DNA read alignment is an integral part of genome study, which has been revolutionised thanks to the growth of Next Generation Sequencing (NGS) technologies. The inherent computational intensity of string matching algorithms such as Smith-Waterman (SmW) and the vast amount of NGS input data, create a...

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Veröffentlicht in:	IEEE transactions on computers 2022-11, Vol.71 (11), p.3018-3031
Hauptverfasser:	Koliogeorgi, Konstantina, Xydis, Sotirios, Gaydadjiev, Georgi, Soudris, Dimitrios
Format:	Artikel
Sprache:	eng
Schlagworte:	Accelerators Algorithms Alignment Bioinformatics Bowtie2 Co-design Communications systems dataflow computing DNA Field programmable gate arrays Genomics Next generation sequencing reconfigurable acceleration Sequential analysis smith waterman Software String matching Task analysis traceback
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