GSR: Simulator - DUDE-Seq

Basic Package Attributes
AttributeValue
Title DUDE-Seq
Short Description Fast, flexible, and robust denoising of nucleotide sequences
Long Description 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.
Homepagehttp://data.snu.ac.kr/pub/dude-seq/
Citations Lee B, Moon T, Yoon S, Weissman T, DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing., PLoS One, 07-27-2017 [ Abstract, cited in PMC ]
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Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation Method
Input
Data Type
File format
Output
Data Type
Sequencing Reads
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
Interface
Development
Tested Platforms
Language
License
GSR Certification

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