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...
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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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