BLEND: A fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis

buir.contributor.authorAlkan, Can
buir.contributor.orcidAlkan, Can|0000-0002-5443-0706
dc.citation.epagelqad004-18en_US
dc.citation.issueNumber1
dc.citation.spagelqad004-1
dc.citation.volumeNumber5
dc.contributor.authorFirtina, C.
dc.contributor.authorPark, J.
dc.contributor.authorAlser, M.
dc.contributor.authorKim, J. S.
dc.contributor.authorCali, D. S.
dc.contributor.authorShahroodi, T.
dc.contributor.authorGhiasi, N. M.
dc.contributor.authorSingh, G.
dc.contributor.authorKanellopoulos, K.
dc.contributor.authorAlkan, Can
dc.contributor.authorMutlu, O.
dc.date.accessioned2024-03-21T14:56:16Z
dc.date.available2024-03-21T14:56:16Z
dc.date.issued2023-01-10
dc.departmentDepartment of Computer Engineering
dc.description.abstractGenerating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the same hash value for similar sets, and (ii) provides the proper mechanisms for using seeds as sets with the SimHash technique to find fuzzy seed matches efficiently. We show the benefits of BLEND when used in read overlapping and read mapping. For read overlapping, BLEND is faster by 2.4×-83.9× (on average 19.3×), has a lower memory footprint by 0.9×-14.1× (on average 3.8×), and finds higher quality overlaps leading to accurate de novo assemblies than the state-of-the-art tool, minimap2. For read mapping, BLEND is faster by 0.8×-4.1× (on average 1.7×) than minimap2. Source code is available at https://github.com/CMU-SAFARI/BLEND. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
dc.description.provenanceMade available in DSpace on 2024-03-21T14:56:16Z (GMT). No. of bitstreams: 1 BLEND_A_fast,_memory-efficient_and_accurate_mechanism_to_find_fuzzy_seed_matches_in_genome_analysis.pdf: 2037417 bytes, checksum: a201d06bb45b53ab2d58599bd2482619 (MD5) Previous issue date: 2023-01-20en
dc.identifier.doi10.1093/nargab/lqad004en_US
dc.identifier.eissn2631-9268en_US
dc.identifier.urihttps://hdl.handle.net/11693/115049en_US
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://dx.doi.org/10.1093/nargab/lqad004
dc.rightsCC BY 4.0 DEED (Attribution 4.0 International)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.source.titleNAR Genomics and Bioinformatics
dc.titleBLEND: A fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
dc.typeArticle

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
BLEND_A_fast,_memory-efficient_and_accurate_mechanism_to_find_fuzzy_seed_matches_in_genome_analysis.pdf
Size:
1.94 MB
Format:
Adobe Portable Document Format

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
2.01 KB
Format:
Item-specific license agreed upon to submission
Description: