BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

PeerJ

article

Gong Cheng¹  Quan Lu³  Ling Ma⁴  Guocai Zhang⁴  Liang Xu⁵  Zongshan Zhou¹ 

[1] Protection Research Center of Pomology, Research Institute of Pomology, Chinese Academy of Agricultural Sciences;Forest Protection Research Institute of Heilongjiang Province;Research Institute of Forest Ecology;School of Forestry, Northeast Forestry University;Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences

关键词: Docker;    Pan-genome;    Biosynthetic gene clusters;    Bacillus amyloliquefaciens;   

DOI  :  10.7717/peerj.3948

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

【 授权许可】

CC BY