MABBI – Research conducted by Ni Kadek Dita Cahyani, Aji Wahyu Anggoro, Muhammad Danie Al Malik, Beginer Subhan, Lalu M. Iqbal Sani and Hawis Madduppa from IPB University, Diponegoro University, Indonesian Biodiversity Foundation (Bionesia), University of California, and Oceanogen Research Center entitled Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: comparative high throughput analysis using different bioinformatic pipelines
The selection of specific bioinformatic pipelines to analyze Next Generation Sequencing (NGS) data is instrumental for generating accurate biological inferences; users should understand the limitations of the pipelines and incorporate existing biodiversity information to evaluate results. Pipelines that maximize the coverage and precision of taxonomic inventories and are in line with local biodiversity characteristics should be preferred. Environmental DNA (eDNA) metabarcoding based on NGS technology is projected to be widely employed for biomonitoring applications and to supplement established ways of monitoring marine biodiversity. In Indonesia, research has concentrated on assessing taxonomic composition in various geographical and environmental situations and on identifying taxa that are susceptible to environmental changes. This study aims to compare four NGS data analysis pipelines (Anacapa, QIIME2 with DADA2, QIIME2 with Deblur and Galaxy) using a 28-sample subset of published eDNA seawater samples collected from seawater across Indonesia. The outputs of the bioinformatics analyzes between the pipelines differ. Anacapa, QIIME2 with DADA2, and Galaxy pipelines provide more comprehensive taxonomic coverage relevant to existing biodiversity records from the regions compared to QIIME2 with Deblur. Anacapa in particular could successfully detect taxa that had not been detected with other pipelines tested. These findings should be taken into account when doing eDNA metabarcoding analyses, especially when assessing marine biodiversity in terms of species diversity and abundance. (Tri/MABBI)
Read more: https://link.springer.com/article/10.1007/s12526-024-01432-w
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