Matches in SemOpenAlex for { <https://semopenalex.org/work/W3086684206> ?p ?o ?g. }
Showing items 1 to 94 of
94
with 100 items per page.
- W3086684206 abstract "Abstract Background In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo assembly of state-of-the-art third generation long DNA reads. Darwin is designed to be hardware-friendly and can be accelerated on specialized computer system hardware to achieve higher performance. Results This work accelerates Darwin on GPUs. Using real Pacbio data, our GPU implementation on Tesla K40 has shown a speedup of 109x vs 8 CPU threads of an Intel Xeon machine and 24x vs 64 threads of IBM Power8 machine. The GPU implementation supports both linear and affine gap, scoring model. The results show that the GPU implementation can achieve the same high speedup for different scoring schemes. Conclusions The GPU implementation proposed in this work shows significant improvement in performance compared to the CPU version, thereby making it accessible for utilization as a practical read overlapper in a DNA assembly pipeline. Furthermore, our GPU acceleration can also be used for performing fast Smith-Waterman alignment between long DNA reads. GPU hardware has become commonly available in the field today, making the proposed acceleration accessible to a larger public. The implementation is available at https://github.com/Tongdongq/darwin-gpu ." @default.
- W3086684206 created "2020-09-21" @default.
- W3086684206 creator A5021955713 @default.
- W3086684206 creator A5032731280 @default.
- W3086684206 creator A5033626149 @default.
- W3086684206 creator A5058128591 @default.
- W3086684206 date "2020-09-01" @default.
- W3086684206 modified "2023-10-10" @default.
- W3086684206 title "GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads" @default.
- W3086684206 cites W1966822396 @default.
- W3086684206 cites W1977512185 @default.
- W3086684206 cites W1982088757 @default.
- W3086684206 cites W1984236772 @default.
- W3086684206 cites W2040132285 @default.
- W3086684206 cites W2055043387 @default.
- W3086684206 cites W2087064593 @default.
- W3086684206 cites W2115324785 @default.
- W3086684206 cites W2115501618 @default.
- W3086684206 cites W2129933858 @default.
- W3086684206 cites W2136651963 @default.
- W3086684206 cites W2144560237 @default.
- W3086684206 cites W2146379626 @default.
- W3086684206 cites W2146696273 @default.
- W3086684206 cites W2160969485 @default.
- W3086684206 cites W2165654401 @default.
- W3086684206 cites W2789784730 @default.
- W3086684206 cites W2797956284 @default.
- W3086684206 cites W2900776157 @default.
- W3086684206 cites W2938304012 @default.
- W3086684206 cites W2981619930 @default.
- W3086684206 doi "https://doi.org/10.1186/s12859-020-03685-1" @default.
- W3086684206 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7495891" @default.
- W3086684206 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32938392" @default.
- W3086684206 hasPublicationYear "2020" @default.
- W3086684206 type Work @default.
- W3086684206 sameAs 3086684206 @default.
- W3086684206 citedByCount "2" @default.
- W3086684206 countsByYear W30866842062023 @default.
- W3086684206 crossrefType "journal-article" @default.
- W3086684206 hasAuthorship W3086684206A5021955713 @default.
- W3086684206 hasAuthorship W3086684206A5032731280 @default.
- W3086684206 hasAuthorship W3086684206A5033626149 @default.
- W3086684206 hasAuthorship W3086684206A5058128591 @default.
- W3086684206 hasBestOaLocation W30866842061 @default.
- W3086684206 hasConcept C111919701 @default.
- W3086684206 hasConcept C117896860 @default.
- W3086684206 hasConcept C121332964 @default.
- W3086684206 hasConcept C13164978 @default.
- W3086684206 hasConcept C145108525 @default.
- W3086684206 hasConcept C173608175 @default.
- W3086684206 hasConcept C2778119891 @default.
- W3086684206 hasConcept C41008148 @default.
- W3086684206 hasConcept C42935608 @default.
- W3086684206 hasConcept C43521106 @default.
- W3086684206 hasConcept C68339613 @default.
- W3086684206 hasConcept C74650414 @default.
- W3086684206 hasConcept C9390403 @default.
- W3086684206 hasConcept C98045186 @default.
- W3086684206 hasConceptScore W3086684206C111919701 @default.
- W3086684206 hasConceptScore W3086684206C117896860 @default.
- W3086684206 hasConceptScore W3086684206C121332964 @default.
- W3086684206 hasConceptScore W3086684206C13164978 @default.
- W3086684206 hasConceptScore W3086684206C145108525 @default.
- W3086684206 hasConceptScore W3086684206C173608175 @default.
- W3086684206 hasConceptScore W3086684206C2778119891 @default.
- W3086684206 hasConceptScore W3086684206C41008148 @default.
- W3086684206 hasConceptScore W3086684206C42935608 @default.
- W3086684206 hasConceptScore W3086684206C43521106 @default.
- W3086684206 hasConceptScore W3086684206C68339613 @default.
- W3086684206 hasConceptScore W3086684206C74650414 @default.
- W3086684206 hasConceptScore W3086684206C9390403 @default.
- W3086684206 hasConceptScore W3086684206C98045186 @default.
- W3086684206 hasIssue "S13" @default.
- W3086684206 hasLocation W30866842061 @default.
- W3086684206 hasLocation W30866842062 @default.
- W3086684206 hasLocation W30866842063 @default.
- W3086684206 hasLocation W30866842064 @default.
- W3086684206 hasOpenAccess W3086684206 @default.
- W3086684206 hasPrimaryLocation W30866842061 @default.
- W3086684206 hasRelatedWork W1507301366 @default.
- W3086684206 hasRelatedWork W1987169484 @default.
- W3086684206 hasRelatedWork W2086643394 @default.
- W3086684206 hasRelatedWork W2100952904 @default.
- W3086684206 hasRelatedWork W2143593481 @default.
- W3086684206 hasRelatedWork W2166164399 @default.
- W3086684206 hasRelatedWork W2307508632 @default.
- W3086684206 hasRelatedWork W2695396743 @default.
- W3086684206 hasRelatedWork W4311833893 @default.
- W3086684206 hasRelatedWork W4317208900 @default.
- W3086684206 hasVolume "21" @default.
- W3086684206 isParatext "false" @default.
- W3086684206 isRetracted "false" @default.
- W3086684206 magId "3086684206" @default.
- W3086684206 workType "article" @default.