Literature DB >> 28945707

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads.

Chuan-Le Xiao1,2,3,4, Ying Chen2, Shang-Qian Xie1,5, Kai-Ning Chen1, Yan Wang1, Yue Han1,6, Feng Luo7, Zhi Xie1.   

Abstract

We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.

Mesh：

Year:  2017        PMID： 28945707     DOI： 10.1038/nmeth.4432

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  16 in total

Review 1.  A window into third-generation sequencing.

Authors:  Eric E Schadt; Steve Turner; Andrew Kasarskis
Journal:  Hum Mol Genet       Date:  2010-09-21       Impact factor: 6.150

2.  Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.

Authors:  Konstantin Berlin; Sergey Koren; Chen-Shan Chin; James P Drake; Jane M Landolin; Adam M Phillippy
Journal:  Nat Biotechnol       Date:  2015-05-25       Impact factor: 54.908

3.  De novo assembly and phasing of a Korean human genome.

Authors:  Jeong-Sun Seo; Arang Rhie; Junsoo Kim; Sangjin Lee; Min-Hwan Sohn; Chang-Uk Kim; Alex Hastie; Han Cao; Ji-Young Yun; Jihye Kim; Junho Kuk; Gun Hwa Park; Juhyeok Kim; Hanna Ryu; Jongbum Kim; Mira Roh; Jeonghun Baek; Michael W Hunkapiller; Jonas Korlach; Jong-Yeon Shin; Changhoon Kim
Journal:  Nature       Date:  2016-10-05       Impact factor: 49.962

4.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Authors:  Chen-Shan Chin; David H Alexander; Patrick Marks; Aaron A Klammer; James Drake; Cheryl Heiner; Alicia Clum; Alex Copeland; John Huddleston; Evan E Eichler; Stephen W Turner; Jonas Korlach
Journal:  Nat Methods       Date:  2013-05-05       Impact factor: 28.547

5.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

6.  Phased diploid genome assembly with single-molecule real-time sequencing.

Authors:  Chen-Shan Chin; Paul Peluso; Fritz J Sedlazeck; Maria Nattestad; Gregory T Concepcion; Alicia Clum; Christopher Dunn; Ronan O'Malley; Rosa Figueroa-Balderas; Abraham Morales-Cruz; Grant R Cramer; Massimo Delledonne; Chongyuan Luo; Joseph R Ecker; Dario Cantu; David R Rank; Michael C Schatz
Journal:  Nat Methods       Date:  2016-10-17       Impact factor: 28.547

7.  Real-time DNA sequencing from single polymerase molecules.

Authors:  John Eid; Adrian Fehr; Jeremy Gray; Khai Luong; John Lyle; Geoff Otto; Paul Peluso; David Rank; Primo Baybayan; Brad Bettman; Arkadiusz Bibillo; Keith Bjornson; Bidhan Chaudhuri; Frederick Christians; Ronald Cicero; Sonya Clark; Ravindra Dalal; Alex Dewinter; John Dixon; Mathieu Foquet; Alfred Gaertner; Paul Hardenbol; Cheryl Heiner; Kevin Hester; David Holden; Gregory Kearns; Xiangxu Kong; Ronald Kuse; Yves Lacroix; Steven Lin; Paul Lundquist; Congcong Ma; Patrick Marks; Mark Maxham; Devon Murphy; Insil Park; Thang Pham; Michael Phillips; Joy Roy; Robert Sebra; Gene Shen; Jon Sorenson; Austin Tomaney; Kevin Travers; Mark Trulson; John Vieceli; Jeffrey Wegener; Dawn Wu; Alicia Yang; Denis Zaccarin; Peter Zhao; Frank Zhong; Jonas Korlach; Stephen Turner
Journal:  Science       Date:  2008-11-20       Impact factor: 47.728

8.  Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Authors:  Sergey Koren; Michael C Schatz; Brian P Walenz; Jeffrey Martin; Jason T Howard; Ganeshkumar Ganapathy; Zhong Wang; David A Rasko; W Richard McCombie; Erich D Jarvis
Journal:  Nat Biotechnol       Date:  2012-07-01       Impact factor: 54.908

9.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.

Authors:  Mark J Chaisson; Glenn Tesler
Journal:  BMC Bioinformatics       Date:  2012-09-19       Impact factor: 3.169

10.  Long-read sequence assembly of the gorilla genome.

Authors:  David Gordon; John Huddleston; Mark J P Chaisson; Christopher M Hill; Zev N Kronenberg; Katherine M Munson; Maika Malig; Archana Raja; Ian Fiddes; LaDeana W Hillier; Christopher Dunn; Carl Baker; Joel Armstrong; Mark Diekhans; Benedict Paten; Jay Shendure; Richard K Wilson; David Haussler; Chen-Shan Chin; Evan E Eichler
Journal:  Science       Date:  2016-04-01       Impact factor: 47.728
View more
  91 in total

1.  LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.

Authors:  Gui-Cai Xu; Tian-Jun Xu; Rui Zhu; Yan Zhang; Shang-Qi Li; Hong-Wei Wang; Jiong-Tang Li
Journal:  Gigascience       Date:  2019-01-01       Impact factor: 6.524

Review 2.  Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

Authors:  Damla Senol Cali; Jeremie S Kim; Saugata Ghose; Can Alkan; Onur Mutlu
Journal:  Brief Bioinform       Date:  2019-07-19       Impact factor: 11.622

3.  Draft genomic sequence of Armillaria gallica 012m: insights into its symbiotic relationship with Gastrodia elata.

Authors:  Mengtao Zhan; Menghua Tian; Weiguang Wang; Ganpeng Li; Xiaokai Lu; Guolei Cai; Haiying Yang; Gang Du; Lishuxin Huang
Journal:  Braz J Microbiol       Date:  2020-06-22       Impact factor: 2.476

Review 4.  Nanopore sequencing technology, bioinformatics and applications.

Authors:  Yunhao Wang; Yue Zhao; Audrey Bollas; Yuru Wang; Kin Fai Au
Journal:  Nat Biotechnol       Date:  2021-11-08       Impact factor: 54.908

5.  Single-molecule long-read transcriptome profiling of Platysternon megacephalum mitochondrial genome with gene rearrangement and control region duplication.

Authors:  Jianjun Liu; Hui Jiang; Jiawei Zan; Yuantian Bao; Jinxiu Dong; Lei Xiong; Liuwang Nie
Journal:  RNA Biol       Date:  2018-09-23       Impact factor: 4.652

6.  Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association.

Authors:  Rong Wang; Yang Yang; Yi Jing; Simon T Segar; Yu Zhang; Gang Wang; Jin Chen; Qing-Feng Liu; Shan Chen; Yan Chen; Astrid Cruaud; Yuan-Yuan Ding; Derek W Dunn; Qiang Gao; Philip M Gilmartin; Kai Jiang; Finn Kjellberg; Hong-Qing Li; Yuan-Yuan Li; Jian-Quan Liu; Min Liu; Carlos A Machado; Ray Ming; Jean-Yves Rasplus; Xin Tong; Ping Wen; Huan-Ming Yang; Jing-Jun Yang; Ye Yin; Xing-Tan Zhang; Yuan-Ye Zhang; Hui Yu; Zhen Yue; Stephen G Compton; Xiao-Yong Chen
Journal:  Nat Ecol Evol       Date:  2021-05-17       Impact factor: 15.460

7.  The tepary bean genome provides insight into evolution and domestication under heat stress.

Authors:  Samira Mafi Moghaddam; Atena Oladzad; Chushin Koh; Larissa Ramsay; John P Hart; Sujan Mamidi; Genevieve Hoopes; Avinash Sreedasyam; Andrew Wiersma; Dongyan Zhao; Jane Grimwood; John P Hamilton; Jerry Jenkins; Brieanne Vaillancourt; Joshua C Wood; Jeremy Schmutz; Sateesh Kagale; Timothy Porch; Kirstin E Bett; C Robin Buell; Phillip E McClean
Journal:  Nat Commun       Date:  2021-05-11       Impact factor: 14.919

8.  Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications.

Authors:  Huiyin Song; Yang Chen; Feng Liu; Nansheng Chen
Journal:  Front Microbiol       Date:  2021-07-02       Impact factor: 5.640

9.  Probiotics: their action against pathogens can be turned around.

Authors:  Lian Gan; Wei-Hua Xu; Yuanyan Xiong; Zhaolin Lv; Jianwei Zheng; Yu Zhang; Jianhao Lin; Jingshu Liu; Shijun Chen; Mengqiu Chen; Qingqi Guo; Junfeng Wu; Jingjie Chen; Zhenhua Su; Jijia Sun; Yuhui He; Chuanhe Liu; Weifang Wang; Willy Verstraete; Patrick Sorgeloos; Tom Defoirdt; Qiwei Qin; Yiying Liu
Journal:  Sci Rep       Date:  2021-06-24       Impact factor: 4.379

10.  Genome and Evolutionary Analysis of Nosema ceranae: A Microsporidian Parasite of Honey Bees.

Authors:  Qiang Huang; Zhi Hao Wu; Wen Feng Li; Rui Guo; Jin Shan Xu; Xiao Qun Dang; Zheng Gang Ma; Yan Ping Chen; Jay D Evans
Journal:  Front Microbiol       Date:  2021-06-02       Impact factor: 5.640
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.