Swabs to genomes: a comprehensive workflow
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Microbiology
- Keywords
- Workflow, Microbial Genomics, Genome Sequencing, Genome Assembly, Bioinformatics
- Copyright
- © 2015 Dunitz 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
- 2015. Swabs to genomes: a comprehensive workflow. PeerJ PrePrints 3:e453v2 https://doi.org/10.7287/peerj.preprints.453v2
Abstract
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
Author Comment
This version of the pre-print, now submitted to PeerJ for review includes a number of changes throughout to reflect feedback from the community and additional testing in-house.