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Published on: September 16, 2019
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences
Ting-Hsuan Wang1, Cheng-Ching Huang1, Jui-Hung Hung1
1Department of Computer Science, College of Computer Science, National Chiao Tung University, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan.
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.
