BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

BMC Bioinformatics

Methodology

Daniel Alonso-Alemany¹  Gabriel Valiente¹  Marinella Marzano²  Monica Santamaria²  Bruno Fosso²  Graziano Pesole³  Pasquale Notarangelo⁴  Alfonso Monaco⁴  Giacinto Donvito⁴ 

[1] Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain;Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, 70126, Bari, Italy;Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, 70126, Bari, Italy;Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, via E. Orabona 4, 70125, Bari, Italy;Center of Excellence in Comparative Genomics, University of Bari “A. Moro”, via E. Orabona, 4, 70125, Bari, Italy;National Institute of Nuclear Physics, via E. Orabona 4, 70125, Bari, Italy;

关键词: Metagenomics;    Bioinformatics;    Microbiome;    Meta-barcoding;    High-Throughput Sequencing;   

DOI  :  10.1186/s12859-015-0595-z

 received in 2015-03-03, accepted in 2015-04-23,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundSubstantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.ResultsBioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).ConclusionBioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.

【 授权许可】

Unknown   
© Fosso et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.