BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

BMC Bioinformatics

Bruno Fosso⁴  Monica Santamaria⁴  Marinella Marzano⁴  Daniel Alonso-Alemany³  Gabriel Valiente³  Giacinto Donvito¹  Alfonso Monaco¹  Pasquale Notarangelo¹  Graziano Pesole² 

[1] National Institute of Nuclear Physics, via E. Orabona 4, Bari 70125, Italy

[2] Center of Excellence in Comparative Genomics, University of Bari “A. Moro”, via E. Orabona, 4, Bari 70125, Italy

[3] Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain

[4] Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari 70126, Italy

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

Others  :  1231822
DOI  :  10.1186/s12859-015-0595-z

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

【 摘 要 】

Background

Substantial 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.

Results

BioMaS (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).

Conclusion

BioMaS 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】

   
2015 Fosso et al.

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