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

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

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

Abstract 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 h

Externí odkaz: https://doaj.org/article/fe6a013bcda049eab4be4d2c23220601

Scheduling with Gaps: New Models and Algorithms

Autor: Chrobak, Marek, Golin, Mordecai, Lam, Tak-Wah, Nogneng, Dorian

We consider scheduling problems for unit jobs with release times, where the number or size of the gaps in the schedule is taken into consideration, either in the objective function or as a constraint. Except for a few papers on energy minimization, t

Externí odkaz: http://arxiv.org/abs/1410.7092

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Autor: Chan, Sze-Hang, Cheung, Jeanno, Wu, Edward, Wang, Heng, Liu, Chi-Man, Zhu, Xiaoqian, Peng, Shaoliang, Luo, Ruibang, Lam, Tak-Wah

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alternative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to o

Externí odkaz: http://arxiv.org/abs/1402.4876

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

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

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and decreasing

Externí odkaz: http://arxiv.org/abs/1305.6760

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Autor: Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F.

Publikováno v: GigaScience 2:10 (2013)

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are av

Externí odkaz: http://arxiv.org/abs/1301.5406