De novo assembly of a haplotype-resolved human genome

Autor: Yu Wang, Haodong Huang, Honglong Wu, Lars Bolund, Laurent C. A. M. Tellier, Xiuqing Zhang, Zheng Huang, Hongzhi Cao, Rasmus Nielsen, Xin Tong, Li Yue, Bo Li, Xiao Liu, Siyang Liu, Ruibang Luo, Yuhui Sun, Guangzhu He, Sun Jing, Shujia Huang, Dan Chen, Yingrui Li, Xun Xu, Jian Li, Songgang Li, Weihua Huang, Jun Wang, Qiang Feng, Anders Krogh, Peng Sun, Karsten Kristiansen, Snezana Drmanac, Gane Ka-Shu Wong, Binghang Liu, Radoje Drmanac, Yinlong Xie, Jian Wang, Hailong Yang, Peng Gao, Huanming Yang, Fang Yang, Hancheng Zheng

Publikováno v: Cao, H, Wu, H, Luo, R, Huang, S, Sun, Y, Tong, X, Xie, Y, Liu, B, Yang, H, Zheng, H, Li, J, Li, B, Wang, Y, Yang, F, Sun, P, Liu, S, Gao, P, Huang, H, Sun, J, Chen, D, He, G, Huang, W, Huang, Z, Li, Y, Tellier, L C A M, Liu, X, Feng, Q, Xu, X, Zhang, X, Bolund, L, Krogh, A, Kristiansen, K, Drmanac, R, Drmanac, S, Nielsen, R, Li, S, Wang, J, Yang, H, Li, Y, Wong, G K-S & Wang, J 2015, ' De novo assembly of a haplotype-resolved human genome ', Nature Biotechnology, vol. 33, no. 6, pp. 617-22 . https://doi.org/10.1038/nbt.3200

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipelin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c051c370dc4b77342e42bb0ac01c0a02
https://doi.org/10.1038/nbt.3200

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Autor: Shengchang Gu, Gengxiong Wu, Weihua Huang, Jordan Patterson, Gane Ka-Shu Wong, Ruibang Luo, Yingrui Li, Shengkang Li, Xun Xu, Yinlong Xie, Shanlin Liu, Jingbo Tang, Tak-Wah Lam, Xin Zhou, Jun Wang, Guangzhu He

Publikováno v: Bioinformatics (Oxford, England). 30(12)

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9e4e9d50ed4b3c04088063296c057e0d
https://pubmed.ncbi.nlm.nih.gov/24532719

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Autor: Yinlong Xie, Yujian Shi, Hao Zhang, Ruibang Luo, Zhu Xiao-qian, Tak-Wah Lam, Bo Wang, Siu-Ming Yiu, Yingrui Li, Shaoliang Peng, Qi Pan, Guangming Liu, Binghang Liu, David W. Cheung, Zhenyu Li, Yanxiang Chen, Jian Wang, Yunjie Liu, Huanming Yang, Jingbo Tang, Jun Wang, Guangzhu He, Xiangke Liao, Changlei Han, Chang Yu, Gengxiong Wu, Yong Liu, Weihua Huang, Yao Lu, Jianying Yuan

Publikováno v: GigaScience
GigaScience, Vol 1, Iss 1, p 18 (2012)

Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a720ce5340e0d4ef4156d71718b1603