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Mar 31, 2021
Data Structures to Represent a Set of k-long DNA Sequences
ACM Computing Surveys Chikhi R, Holub J, Medvedev P The analysis of biological sequencing data has been one of the biggest applications...
Dec 1, 2020
Data structures based on kmers for querying large collections of sequencing data sets
Genome Res Marchet C, Boucher C, Puglisi SJ, Medvedev P, Salson M, Chikhi R High-throughput sequencing data sets are usually deposited...
Sep 6, 2020
Disk Compression of k-mer Sets
WABI Rahman A, Chikhi R, Medvedev P K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as...
Jun 30, 2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Bioinformatics Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Motivation: In this work we present REINDEER, a novel computational...
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