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image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Journal of Computati...arrow_drop_down
image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
Journal of Computational Biology
Article . 2016 . Peer-reviewed
License: Mary Ann Liebert TDM
Data sources: Crossref
DBLP
Article . 2020
Data sources: DBLP
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Computational Performance Assessment of k-mer Counting Algorithms

Authors: Jose Nelson Perez Castillo; Miguel Gutierrez; Nelson Enrique Vera Parra;

Computational Performance Assessment of k-mer Counting Algorithms

Abstract

This article is about the assessment of several tools for k-mer counting, with the purpose to create a reference framework for bioinformatics researchers to identify computational requirements, parallelizing, advantages, disadvantages, and bottlenecks of each of the algorithms proposed in the tools. The k-mer counters evaluated in this article were BFCounter, DSK, Jellyfish, KAnalyze, KHMer, KMC2, MSPKmerCounter, Tallymer, and Turtle. Measured parameters were the following: RAM occupied space, processing time, parallelization, and read and write disk access. A dataset consisting of 36,504,800 reads was used corresponding to the 14th human chromosome. The assessment was performed for two k-mer lengths: 31 and 55. Obtained results were the following: pure Bloom filter-based tools and disk-partitioning techniques showed a lesser RAM use. The tools that took less execution time were the ones that used disk-partitioning techniques. The techniques that made the major parallelization were the ones that used disk partitioning, hash tables with lock-free approach, or multiple hash tables.

Related Organizations
Keywords

Chromosomes, Human, Pair 14, Computational Biology, Humans, Sequence Analysis, DNA, Sensitivity and Specificity, Algorithms, Software

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Powered by OpenAIRE graph
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
15
Top 10%
Top 10%
Top 10%
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