The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbia...The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential.However,existing clustering algorithms perform poorly on long genomic sequences.In this article,we present Gclust,a parallel program for clustering complete or draft genomic sequences,where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays(SSAs).Moreover,genome identity measures between two sequences are calculated based on their maximal exact matches(MEMs).In this paper,we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets.Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust.We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust.展开更多
基金the National Key R&D Program of China(Grant Nos.2018YFB0203903,2016YFC0503607,and 2016YFB0200300)the National Natural Science Foundation of China(Grant Nos.31771466 and 61702476)+3 种基金the Transformation Project in Scientific and Technological Achievements of Qinghai Province,China(Grant No.2016-SF-127)the Special Project of Informatization(Grant No.XXH13504-08)the Strategic Pilot Science and Technology Project(Grant No.XDA12010000)the 100-Talents Program(awarded to BN)of the Chinese Academy of Sciences,China.
文摘The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential.However,existing clustering algorithms perform poorly on long genomic sequences.In this article,we present Gclust,a parallel program for clustering complete or draft genomic sequences,where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays(SSAs).Moreover,genome identity measures between two sequences are calculated based on their maximal exact matches(MEMs).In this paper,we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets.Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust.We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust.
