{"title":"Data Structures for SMEM-Finding in the PBWT.","authors":"Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi","doi":"10.1007/978-3-031-43980-3_8","DOIUrl":"10.1007/978-3-031-43980-3_8","url":null,"abstract":"<p><p>The positional Burrows-Wheeler Transform (PBWT) was presented as a means to find set-maximal exact matches (SMEMs) in haplotype data via the computation of the divergence array. Although run-length encoding the PBWT has been previously considered, storing the divergence array along with the PBWT in a compressed manner has not been as rigorously studied. We define two queries that can be used in combination to compute SMEMs, allowing us to define smaller data structures that support one or both of these queries. We combine these data structures, enabling the PBWT and the divergence array to be stored in a manner that allows for finding SMEMs. We estimate and compare the memory usage of these data structures, leading to one data structure that is most memory efficient. Lastly, we implement this data structure and compare its performance to prior methods using various datasets taken from the 1000 Genomes Project data.</p>","PeriodicalId":520001,"journal":{"name":"International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)","volume":"14240 ","pages":"89-101"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11325217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Space-time Trade-offs for the LCP Array of Wheeler DFAs.","authors":"Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza","doi":"10.1007/978-3-031-43980-3_12","DOIUrl":"10.1007/978-3-031-43980-3_12","url":null,"abstract":"<p><p>Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP array requires <math><mrow><mi>O</mi> <mfenced><mrow><mi>n</mi> <mi>log</mi> <mi>n</mi></mrow> </mfenced> </mrow> </math> bits, <math><mi>n</mi></math> being the number of states, while the compact representation of Wheeler DFAs often requires much less space. In particular, the BOSS representation of a de Bruijn graph only requires a linear number of bits, if the size of alphabet is constant. In this paper, we propose a sampling technique that allows to access an entry of the LCP array in logarithmic time by only storing a linear number of bits. We use our technique to provide a space-time tradeoff to compute matching statistics on a Wheeler DFA. In addition, we show that by augmenting the BOSS representation of a <math><mi>k</mi></math> -th order de Bruijn graph with a linear number of bits we can navigate the underlying variable-order de Bruijn graph in time logarithmic in <math><mi>k</mi></math> , thus improving a previous bound by Boucher et al. which was linear in <math><mi>k</mi></math> [DCC 2015].</p>","PeriodicalId":520001,"journal":{"name":"International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)","volume":"14240 ","pages":"143-156"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">KATKA: A KRAKEN-like tool with <ns0:math><ns0:mi>k</ns0:mi></ns0:math> given at query time.","authors":"Travis Gagie, Sana Kashgouli, Ben Langmead","doi":"10.1007/978-3-031-20643-6_14","DOIUrl":"10.1007/978-3-031-20643-6_14","url":null,"abstract":"<p><p>We describe a new tool, KATKA, that stores a phylogenetic tree <math><mi>T</mi></math> such that later, given a pattern <math><mi>P</mi> <mo>[</mo> <mn>1</mn> <mo>.</mo> <mo>.</mo> <mi>m</mi> <mo>]</mo></math> and an integer <math><mi>k</mi></math> , it can quickly return the root of the smallest subtree of <math><mi>T</mi></math> containing all the genomes in which the <i>k</i>-mer <math><mi>P</mi> <mo>[</mo> <mi>i</mi> <mo>.</mo> <mo>.</mo> <mi>i</mi> <mo>+</mo> <mi>k</mi> <mo>-</mo> <mn>1</mn> <mo>]</mo></math> occurs, for <math><mn>1</mn> <mo>≤</mo> <mi>i</mi> <mo>≤</mo> <mi>m</mi> <mo>-</mo> <mi>k</mi> <mo>+</mo> <mn>1</mn></math> . This is similar to KRAKEN's functionality but with <math><mi>k</mi></math> given at query time instead of at construction time.</p>","PeriodicalId":520001,"journal":{"name":"International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)","volume":"13617 ","pages":"191-197"},"PeriodicalIF":0.0,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11288484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}