Analysis of Illumina MiSeq metabarcoding data: application to benthic indices for environmental monitoring
Aylagas, E.; Rodríguez-Ezpeleta, N. (2016). Analysis of Illumina MiSeq metabarcoding data: application to benthic indices for environmental monitoring, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 237-249. https://dx.doi.org/10.1007/978-1-4939-3774-5_16
In: Bourlat, S.J. (Ed.) (2016). Marine genomics: methods and protocols. Methods in Molecular Biology, 1452. Humana Press/Springer Science+Business Media, Inc: New York. ISBN 978-1-4939-3772-1. 253 pp. https://dx.doi.org/10.1007/978-1-4939-3774-5, more
In: Methods in Molecular Biology. Humana Press. ISSN 1064-3745, more
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| Author keywords |
Marine benthic macroinvertebrates; Amplicon sequencing CO1; Folmer region; MiSeq |
| Authors | | Top |
- Aylagas, E.
- Rodríguez-Ezpeleta, N.
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| Abstract |
This protocol details the analysis of Illumina MiSeq amplicon libraries derived from marine benthic macroinvertebrate samples and based on two barcodes of the mitochondrial cytochrome oxidase 1 (CO1) gene: a “short region,” covered by overlapping forward and reverse reads and a “long region” for which forward and reverse reads do not overlap. Aside from providing guidelines for analyzing both types of amplicons, we show how amplicon reads can be used for the calculation of benthic indices for environmental monitoring. |
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