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

, , , , ,
1 Protection Research Center of Pomology, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
2 Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
3 School of Forestry, Northeast Agricultural University, Harbin, China
4 Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
DOI
10.7287/peerj.preprints.3040v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Genomics, Microbiology
Keywords
Docker, pan-genome, biosynthetic gene clusters, Bacillus amyloliquefaciens
Copyright
© 2017 Cheng et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Cheng G, Lu Q, Ma L, Zhang G, Xu L, Zhou Z. 2017. BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters. PeerJ Preprints 5:e3040v1

Abstract

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

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

The command line and tip of BGDMdocker

DOI: 10.7287/peerj.preprints.3040v1/supp-1