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Genome Research|August 21, 2008
Mapping short DNA sequencing reads and calling variants using mapping quality scoresHeng Li, Jue Ruan, Richard DurbinGenomics, Proteomics & Bioinformatics|August 29, 2024
BSAlign: A Library for Nucleotide Sequence AlignmentHaojing Shao, Jue RuanNucleic Acids Research|November 9, 2006
PigGIS: Pig Genomic Informatics SystemJue Ruan, Yiran Guo, Heng Li, et al.Bioinformatics (Oxford, England)|June 10, 2009
The Sequence Alignment/Map format and SAMtoolsHeng Li, Bob Handsaker, Alec Wysoker, et al.Bioinformatics (Oxford, England)|September 4, 2012
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq readsZechen Chong, Jue Ruan, Chung-I WuJournal of Genetics and Genomics = Yi Chuan Xue Bao|May 28, 2023
GAEP: a comprehensive genome assembly evaluating pipelineYong Zhang, Hong-Wei Lu, Jue RuanGigabyte (Hong Kong, China)|November 14, 2024
TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment methodPeiyu Zong, Wenpeng Deng, Jian Liu, et al.Advanced Science (Weinheim, Baden-Wurttemberg, Germany)|June 14, 2024
Overcoming the High Error Rate of Composite DNA Letters-Based Digital Storage through Soft-Decision DecodingYaping Xu, Lulu Ding, Shigang Wu, et al.Gigabyte (Hong Kong, China)|February 24, 2023
SMARTdenovo: a de novo assembler using long noisy readsHailin Liu, Shigang Wu, Alun Li, et al.Pageof 300