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Maël Kerbiriou

dblp:214/3929 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2021
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
approximate membership query
0.512021
BLight: efficient exact associative structure for k-mers · Bioinform. 2021
Bioinformatics and computational biology
sequence analysis
0.512021
BLight: efficient exact associative structure for k-mers · Bioinform. 2021
Bioinformatics and computational biology › sequence analysis
sequence indexing
0.512021
BLight: efficient exact associative structure for k-mers · Bioinform. 2021

Methods — techniques the papers use, named apart from their topics

compact static index · 0.5bit-packed representation · 0.5
YearPublicationVenuePosition
2021 BLight: efficient exact associative structure for k-mers
abstract
MOTIVATION: A plethora of methods and applications share the fundamental need to associate information to words for high-throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can be memory expensive. Recent works take advantage of overlaps between k-mers to leverage this challenge. Yet, existing data structures are either unable to associate information to k-mers or are not lightweight enough. RESULTS: We present BLight, a static and exact data structure able to associate unique identifiers to k-mers and determine their membership in a set without false positive that scales to huge k-mer sets with a low memory cost. This index combines an extremely compact representation along with very fast queries. Besides, its construction is efficient and needs no additional memory. Our implementation achieves to index the k-mers from the human genome using 8 GB of RAM (23 bits per k-mer) within 10 min and the k-mers from the large axolotl genome using 63 GB of memory (27 bits per k-mer) within 76 min. Furthermore, while being memory efficient, the index provides a very high throughput: 1.4 million queries per second on a single CPU or 16.1 million using 12 cores. Finally, we also present how BLight can practically represent metagenomic and transcriptomic sequencing data to highlight its wide applicative range. AVAILABILITY AND IMPLEMENTATION: We wrote the BLight index as an open source C++ library under the AGPL3 license available at github.com/Malfoy/BLight. It is designed as a user-friendly library and comes along with code usage samples.
Camille Marchet, Maël Kerbiriou, Antoine Limasset
Bioinform.2