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PIMBA: A PIpeline for MetaBarcoding Analysis

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Advances in Bioinformatics and Computational Biology (BSB 2021)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13063))

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Abstract

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, PEMA, and mBRAVE have been widely used in ecological studies, however, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the software mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines. PIMBA’s implementation is available at https://github.com/reinator/pimba.

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Author information

Authors and Affiliations

  1. Instituto Tecnológico Vale, Belém, Pará, Brazil

    Renato R. M. Oliveira, Raíssa Silva, Gisele L. Nunes & Guilherme Oliveira

  2. Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil

    Renato R. M. Oliveira

Authors
  1. Renato R. M. Oliveira
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  2. Raíssa Silva
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  3. Gisele L. Nunes
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  4. Guilherme Oliveira
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Corresponding author

Correspondence to Guilherme Oliveira .

Editor information

Editors and Affiliations

  1. Leipzig University, Leipzig, Sachsen, Germany

    Peter F. Stadler

  2. University of Brasília, Brasilia, Brazil

    Maria Emilia M. T. Walter

  3. CINVESTAV, Irapuato, Mexico

    Maribel Hernandez-Rosales

  4. Universidade de Brasilia, Brasilia, Brazil

    Marcelo M. Brigido

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Oliveira, R.R.M., Silva, R., Nunes, G.L., Oliveira, G. (2021). PIMBA: A PIpeline for MetaBarcoding Analysis. In: Stadler, P.F., Walter, M.E.M.T., Hernandez-Rosales, M., Brigido, M.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2021. Lecture Notes in Computer Science(), vol 13063. Springer, Cham. https://doi.org/10.1007/978-3-030-91814-9_10

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  • DOI: https://doi.org/10.1007/978-3-030-91814-9_10

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  • Print ISBN: 978-3-030-91813-2

  • Online ISBN: 978-3-030-91814-9

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