2026-09-21T07:12:43Z https://www.ideals.illinois.edu/oai-pmh

oai:www.ideals.illinois.edu:2142/101639 2023-07-11 col_2142_5131 com_2142_5130

Chen, Deming Li, Huiren 2018-09-27T16:28:01Z 2018-09-27T16:28:01Z 2020-09-28T09:15:24Z 2018-05-15 2018-08 k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. We achieved 4.03x speedup using one GTX 1080 Ti with one CPU (Xeon E5-2603) thread and 5.88x speedup using one GPU with four CPU threads over KMC2 running on a single CPU thread. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations. Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-08-01 The student, Huiren Li, accepted the attached license on 2018-05-14 at 19:09. The student, Huiren Li, submitted this Thesis for approval on 2018-05-14 at 19:13. This Thesis was approved for publication on 2018-05-15 at 09:42. DSpace SAF Submission Ingestion Package generated from Vireo submission #12571 on 2018-09-27 at 11:15:40 Made available in DSpace on 2018-09-27T16:28:01Z (GMT). No. of bitstreams: 2 LI-THESIS-2018.pdf: 303460 bytes, checksum: b65c6cb30886988a436e4bde92422b80 (MD5) LICENSE.txt: 4206 bytes, checksum: 7cac7663a7c217c758442af8d5fa3399 (MD5) Previous issue date: 2018-05-15 Embargo set by: Seth Robbins for item 107736 Lift date: 2020-09-27T16:28:07Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 107736 Lift date: 2020-09-27T16:30:34Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 107736 Lift date: 2020-09-27T16:31:43Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 107736 Lift date: 2020-09-27T16:34:29Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system U of I Only Restriction Lifted for Item 107736 on 2020-09-28T09:15:24Z. application/pdf http://hdl.handle.net/2142/101639 en Copyright 2018 Huiren Li k-mer counting GPU acceleration GPU acceleration of advanced K-mer counting for computational genomics text text Electrical & Computer Eng Electrical & Computer Engr University of Illinois at Urbana-Champaign Thesis M.S.