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Data Structures to Represent a Set of k -long DNA Sequences

, , and . ACM Computing Surveys, 54 (1): 1--22 (April 2021)
DOI: 10.1145/3445967

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TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes., , and . CoRR, (2016)Data structures to represent sets of k-long DNA sequences., , and . CoRR, (2019)Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads., and . RECOMB, volume 4955 of Lecture Notes in Computer Science, page 50-64. Springer, (2008)Using state machines to model the Ion Torrent sequencing process and to improve read error rates., and . Bioinform., 29 (13): 344-351 (2013)Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers., , , , and . J. Comput. Biol., 18 (11): 1625-1634 (2011)Modeling biological problems in computer science: a case study in genome assembly.. Briefings Bioinform., 20 (4): 1376-1383 (2019)Representation of k-mer Sets Using Spectrum-Preserving String Sets., and . RECOMB, volume 12074 of Lecture Notes in Computer Science, page 152-168. Springer, (2020)The plane-width of graphs., , and . J. Graph Theory, 68 (3): 229-245 (2011)Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics., and . Bioinform., 35 (3): 415-420 (2019)Complexity of independent set reconfigurability problems., , and . Theor. Comput. Sci., (2012)