Fast and accurate long-read assembly with wtdbg2 von Ruan, Jue, Li, Heng

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Mapping short DNA sequencing reads and calling variants using mapping quality scores von Li, Heng, Ruan, Jue, Durbin, Richard

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Penaeid shrimp genome provides insights into benthic adaptation and frequent molting von Zhang, Xiaojun, Yuan, Jianbo, Sun, Yamin, Li, Shihao, Gao, Yi, Yu, Yang, Liu, Chengzhang, Wang, Quanchao, Lv, Xinjia, Zhang, Xiaoxi, Ma, Ka Yan, Wang, Xiaobo, Lin, Wenchao, Wang, Long, Zhu, Xueli, Zhang, Chengsong, Zhang, Jiquan, Jin, Songjun, Yu, Kuijie, Kong, Jie, Xu, Peng, Chen, Jack, Zhang, Hongbin, Sorgeloos, Patrick, Sagi, Amir, Alcivar-Warren, Acacia, Liu, Zhanjiang, Wang, Lei, Ruan, Jue, Chu, Ka Hou, Liu, Bin, Li, Fuhua, Xiang, Jianhai

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Population sequencing enhances understanding of tea plant evolution von Wang, Xinchao, Feng, Hu, Chang, Yuxiao, Ma, Chunlei, Wang, Liyuan, Hao, Xinyuan, Li, A’lun, Cheng, Hao, Wang, Lu, Cui, Peng, Jin, Jiqiang, Wang, Xiaobo, Wei, Kang, Ai, Cheng, Zhao, Sheng, Wu, Zhichao, Li, Youyong, Liu, Benying, Wang, Guo-Dong, Chen, Liang, Ruan, Jue, Yang, Yajun

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The Sequence Alignment/Map format and SAMtools von Li, Heng, Handsaker, Bob, Wysoker, Alec, Fennell, Tim, Ruan, Jue, Homer, Nils, Marth, Gabor, Abecasis, Goncalo, Durbin, Richard

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DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies von Ye, Chengxi, Hill, Christopher M., Wu, Shigang, Ruan, Jue, Ma, Zhanshan (Sam)

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SMARTdenovo: a de novo assembler using long noisy reads von Liu, Hailin, Wu, Shigang, Li, Alun, Ruan, Jue

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The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution von Liu, Hailin, Wang, Xiaobo, Wang, Guibin, Cui, Peng, Wu, Shigang, Ai, Cheng, Hu, Nan, Li, Alun, He, Bing, Shao, Xiujuan, Wu, Zhichao, Feng, Hu, Chang, Yuxiao, Mu, Desheng, Hou, Jing, Dai, Xiaogang, Yin, Tongming, Ruan, Jue, Cao, Fuliang

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Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration von Shao, Yong, Wang, Xiao-Bo, Zhang, Jin-Jin, Li, Ming-Li, Wu, Shou-Song, Ma, Xi-Yao, Wang, Xue, Zhao, Hui-Fang, Li, Yuan, Zhu, Helen He, Irwin, David M., Wang, De-Peng, Zhang, Guo-Jie, Ruan, Jue, Wu, Dong-Dong

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African lungfish genome sheds light on the vertebrate water-to-land transition von Wang, Kun, Wang, Jun, Zhu, Chenglong, Yang, Liandong, Ren, Yandong, Ruan, Jue, Fan, Guangyi, Hu, Jiang, Xu, Wenjie, Bi, Xupeng, Zhu, Youan, Song, Yue, Chen, Huatao, Ma, Tiantian, Zhao, Ruoping, Jiang, Haifeng, Zhang, Bin, Feng, Chenguang, Yuan, Yuan, Gan, Xiaoni, Li, Yongxin, Zeng, Honghui, Liu, Qun, Zhang, Yaolei, Shao, Feng, Hao, Shijie, Zhang, He, Xu, Xun, Liu, Xin, Wang, Depeng, Zhu, Min, Zhang, Guojie, Zhao, Wenming, Qiu, Qiang, He, Shunping, Wang, Wen

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A super pan-genomic landscape of rice von Shang, Lianguang, Li, Xiaoxia, He, Huiying, Yuan, Qiaoling, Song, Yanni, Wei, Zhaoran, Lin, Hai, Hu, Min, Zhao, Fengli, Zhang, Chao, Li, Yuhua, Gao, Hongsheng, Wang, Tianyi, Liu, Xiangpei, Zhang, Hong, Zhang, Ya, Cao, Shuaimin, Yu, Xiaoman, Zhang, Bintao, Zhang, Yong, Tan, Yiqing, Qin, Mao, Ai, Cheng, Yang, Yingxue, Zhang, Bin, Hu, Zhiqiang, Wang, Hongru, Lv, Yang, Wang, Yuexing, Ma, Jie, Wang, Quan, Lu, Hongwei, Wu, Zhe, Liu, Shanlin, Sun, Zongyi, Zhang, Hongliang, Guo, Longbiao, Li, Zichao, Zhou, Yongfeng, Li, Jiayang, Zhu, Zuofeng, Xiong, Guosheng, Ruan, Jue, Qian, Qian

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LRScaf: improving draft genomes using long noisy reads von Qin, Mao, Wu, Shigang, Li, Alun, Zhao, Fengli, Feng, Hu, Ding, Lulu, Ruan, Jue

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KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost von Zhou, Qian, Ji, Fahu, Lin, Dongxiao, Liu, Xianming, Zhu, Zexuan, Ruan, Jue

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Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads von ZECHEN CHONG, JUE RUAN, WU, Chung-I

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NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads von Hu, Jiang, Wang, Zhuo, Sun, Zongyi, Hu, Benxia, Ayoola, Adeola Oluwakemi, Liang, Fan, Li, Jingjing, Sandoval, José R, Cooper, David N, Ye, Kai, Ruan, Jue, Xiao, Chuan-Le, Wang, Depeng, Wu, Dong-Dong, Wang, Sheng

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En Route to Completion: What Is An Ideal Reference Genome? von Pan, Weihua, Ruan, Jue

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HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation von Hu, Kang, Ni, Peng, Xu, Minghua, Zou, You, Chang, Jianye, Gao, Xin, Li, Yaohang, Ruan, Jue, Hu, Bin, Wang, Jianxin

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Overcoming the High Error Rate of Composite DNA Letters‐Based Digital Storage through Soft‐Decision Decoding von Xu, Yaping, Ding, Lulu, Wu, Shigang, Ruan, Jue

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TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method von Zong, Peiyu, Deng, Wenpeng, Liu, Jian, Ruan, Jue

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Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes von Jia, Hangxing, Tan, Shengjun, Cai, Yingao, Guo, Yanyan, Shen, Jieyu, Zhang, Yaqiong, Ma, Huijing, Zhang, Qingzhu, Chen, Jinfeng, Qiao, Gexia, Ruan, Jue, Zhang, Yong E.

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