MakeHub:Fully Automated Generation of UCSC Genome Browser Assembly Hubs

作     者：Katharina Jasmin Hoff 

作者机构：University of GreifswaldInstitute for Mathematics and Computer Science17489 GreifswaldGermany University of GreifswaldCenter for Functional Genomics of Microbes17489 GreifswaldGermany 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2019年第17卷第5期

页      面：546-549页

核心收录：

学科分类：0710[理学-生物学] 0711[理学-系统科学] 07[理学] 1001[医学-基础医学(可授医学、理学学位)] 0714[理学-统计学（可授理学、经济学学位）] 0703[理学-化学] 0701[理学-数学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：US National Institutes of Health(Grant No.HG000783),gave rise to the development of MakeHub Universitat Greifswald,Germany. 

主　　题：Genome annotation Annotation visualization RNA-seq Genome browser 

摘      要：Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics.This audience requires tools that are easy to use.Such need has been addressed by several genome annotation tools and pipelines.Visualizing resulting annotation is a crucial step of quality control.The UCSC Genome Browser is a powerful and popular genome visualization tool.Assembly Hubs,which can be hosted on any publicly available web server,allow browsing genomes via UCSC Genome Browser servers.The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available.However,the number of steps for creating a novel Assembly Hub is large.In some cases,the format of input files needs to be adapted,which is a difficult task for scientists without programming background.Here,we describe Make Hub,a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion.The pipeline also allows extending previously created Hubs by additional tracks.Make Hub is freely available for downloading at https://***/Gaius-Augustus/Make Hub.