BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data

Daniel Morais; Luiz F W Roesch; Marc Redmile-Gordon; Fausto G Santos; Petr Baldrian; Fernando D Andreote; Victor S Pylro

doi:10.7717/peerj.5299

BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data

PeerJ. 2018 Jul 30:6:e5299. doi: 10.7717/peerj.5299. eCollection 2018.

Authors

Daniel Morais¹, Luiz F W Roesch², Marc Redmile-Gordon³, Fausto G Santos⁴, Petr Baldrian¹, Fernando D Andreote⁵, Victor S Pylro^{5

6}

Affiliations

¹ Institute of Microbiology of the CAS, Prague, Czech Republic.
² Centro para Pesquisa Interdisciplinar em Biotecnologia, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil.
³ Natural England, Sheffield, United Kingdom.
⁴ Biosystems Informatics and Genomics, Instituto René Rachou, Belo Horizonte, Brazil.
⁵ Soil Department, "Luiz de Queiroz" College of Agriculture - ESALQ/USP, Piracicaba, São Paulo, Brazil.
⁶ Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil.

Abstract

Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation to process these huge datasets. The demand on system resources usually requires migrating from Windows to Linux-based operating systems and prior familiarity with command-line interfaces. To overcome this barrier, we developed a fully automated and easy-to-install package as well as a complete, easy-to-follow pipeline for microbial metataxonomic analysis operating in the Windows Subsystem for Linux (WSL)-Bioinformatics Through Windows (BTW). BTW combines several open-access tools for processing marker gene data, including 16S rRNA, bringing the user from raw sequencing reads to diversity-related conclusions. It includes data quality filtering, clustering, taxonomic assignment and further statistical analyses, directly in WSL, avoiding the prior need of migrating from Windows to Linux. BTW is expected to boost the use of NGS amplicon data by facilitating rapid access to a set of bioinformatics tools for Windows users. Moreover, several Linux command line tools became more reachable, which will enhance bioinformatics accessibility to a wider range of researchers and practitioners in the life sciences and medicine. BTW is available in GitHub (https://github.com/vpylro/BTW). The package is freely available for noncommercial users.

Keywords: 16S rRNA; Marker gene; Metataxonomics; Microbiome; Windows.

Grants and funding

This work was supported by the Brazilian Microbiome Project, the National Institute of Science and Technology: Microbiome and the Ministry of Education, Youth and Sports of the Czech Republic grant LM2015055 to Petr Baldrian and Daniel Morais. Victor Satler Pylro receives fellowship from FAPESP (Process 14/50320-4 and 16/02219-8). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.