Abstract
DUDE-Seq considers the correction of errors from nucleotide sequences produced by next-generation sequencing. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and provides an effective means for correcting substitution and homopolymer indel errors. Our experimental studies with real and simulated data sets suggest that the proposed DUDE-Seq outperforms existing alternatives in terms of error-correction capabilities, time efficiency, as boosting the reliability of downstream analyses. Further, DUDE-Seq is universally applicable across different sequencing platforms and analysis pipelines by a simple update of the noise model.
Algorithm
DUDE-Seq adopts an universal algorithm called Discrete Universal DEnoiser (DUDE) to the DNA sequence error correction problem. The semi-stochastic modeling approach from the DUDE framework naturally fits the setting of DNA sequence denoising problems.
$\small\hat{X}_{i}(z^{n})=\underset{\hat{x}\in\mathcal{X}}{\operatorname{arg\,min}}\,\mathbf{m}^T(z^n,z_{i-k}^{i-1},z_{i+1}^{i+k})\mathbf{\Pi}^{-1}[\lambda_{\hat{x}}\odot\pi_{z_i}]$
Paper
Byunghan Lee, Taesup Moon*, Sungroh Yoon*, and Tsachy Weissman, "DUDE-Seq: Fast, Flexible, and Robust Denoising for Targeted Amplicon Sequencing," PLOS ONE, 12(7): e0181463, July 2017.
Code
DUDE-Seq uses the following dependencies: libboost-dev, libgsl0-dev, liblapack-dev, zlib1g-dev.
[code] [web]
Dataset
[P1-P8]
[A5]
[S5]
[Q19-Q31]
[Π]
SRA: SRP000570 (SRS002051-SRS002053)
ENA: PRJEB6244 (ERS671332-ERS671344)