Improving performance of BWA alignment of short sequences with coroutines
In: IT ; 21068; (2021)
Online
Hochschulschrift
Zugriff:
For the Burrows-Wheeler Aligner (BWA), previous experimentation has shown that alignment of short sequences (reads) can benefit fromincreased instruction level parallelism (ILP) using hyperthreading.This thesis investigates and demonstrates that one can increase the performance of short read alignemnt with BWA without hyperthreading enabled, by employing coroutines in order to increase ILP. Analyzing performance when aligning short reads shows that stalls are concentrated to a specific part of the codebase, namely the functions that are used to give an interval of occurrences using the Burrows-Wheeler Transform. By interleaving the BWT lookups from the processingof several separate reads with coroutines, a speedup of 1.28 wasachieved compared to an optimized version of BWA, or 1.51 compared tothe original version.
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Improving performance of BWA alignment of short sequences with coroutines
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Autor/in / Beteiligte Person: | Jonsson, David |
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Quelle: | IT ; 21068; (2021) |
Veröffentlichung: | Uppsala universitet, Institutionen för informationsteknologi, 2021 |
Medientyp: | Hochschulschrift |
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