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Ting-Hsuan Wang

dblp:45/10202 · DBLP profile ↗
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1ranked-venue papers
1as 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 first-author · 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 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis › sequencing data processing
adapter trimming
0.512021
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences · Bioinform. 2021
Bioinformatics and computational biology › sequence analysis
sequencing data processing
0.512021
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences · Bioinform. 2021

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

multithreading · 0.5SIMD · 0.5
YearPublicationVenuePosition
2021 EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences
abstract
MOTIVATION: Cross-sample comparisons or large-scale meta-analyses based on the next generation sequencing (NGS) involve replicable and universal data preprocessing, including removing adapter fragments in contaminated reads (i.e. adapter trimming). While modern adapter trimmers require users to provide candidate adapter sequences for each sample, which are sometimes unavailable or falsely documented in the repositories (such as GEO or SRA), large-scale meta-analyses are therefore jeopardized by suboptimal adapter trimming. RESULTS: Here we introduce a set of fast and accurate adapter detection and trimming algorithms that entail no a priori adapter sequences. These algorithms were implemented in modern C++ with SIMD and multithreading to accelerate its speed. Our experiments and benchmarks show that the implementation (i.e. EARRINGS), without being given any hint of adapter sequences, can reach comparable accuracy and higher throughput than that of existing adapter trimmers. EARRINGS is particularly useful in meta-analyses of a large batch of datasets and can be incorporated in any sequence analysis pipelines in all scales. AVAILABILITY AND IMPLEMENTATION: EARRINGS is open-source software and is available at https://github.com/jhhung/EARRINGS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Ting-Hsuan Wang, Cheng-Ching Huang, Jui-Hung Hung
Bioinform.1