The iBioGen toolkit is currently under preparation and will include:
- Standardized field and lab protocols for next generation biodiversity monitoring
- Open-source pipelines for processing high throughput sequence datasets
- Software for analysis of community-level genetic data
- Online resources for training
- Review and opinion papers that will promote methodological unification and theoretical synthesis in the field of biodiversity genomics
In the meantime, we provide below some links to relevant protocols, software and publications generated by our research teams that you may find useful.
- Standardized field and lab protocols for next generation biodiversity monitoring
- Open-source pipelines for processing high throughput sequence datasets
- Software for analysis of community-level genetic data
- Online resources for training
- Review and opinion papers that will promote methodological unification and theoretical synthesis in the field of biodiversity genomics
In the meantime, we provide below some links to relevant protocols, software and publications generated by our research teams that you may find useful.
SOIL EXTRACTION
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For specimen extractions from soil samples we follow the Flotation – Berlese – Flotation protocol of Arribas et al. (Methods in Ecology and Evolution, 2016, 7, 1071-1081).
Specimens are extracted from the soil matrix by flotation in a large water container, after which floating debris is subjected to drying in Berlese trays. Subsequently, the collected specimens are freed from remaining debris in a second round of flotation. For more details, please download the Arribas et al. (2016) article below. |
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metaMATE
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This software is designed to form part of a metabarcoding pipeline that uses a mitochondrial coding gene, such as CO1, to filter out nuclear mitochondrial pseudogenes. It does this by identifying control sequences then evaluating the effects of abundance thresholds over different dataset partitioning strategies on the rates of valid read recovery and invalid read removal. The software allows careful decisions on the adequate metabarcoding filtering strategy for specific research objectives, improving the reliability of intraspecific genetic information derived from metabarcoding data.
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Development stage: In final stages of development and review
Citation: Andújar, C., Creedy, T.J., Arribas, P., López, H., Salces-Castellano, A., Pérez-Delgado, A., Vogler, A.P. & B.C. Emerson (in review). NUMT dumping: validated removal of nuclear pseudogenes from mitochondrial metabarcode data. Molecular Ecology Resources. Available in bioRxiv |
'iBioGen' R package
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Software for the study of island biodiversity dynamics from genomic data. It is composed of a suite of tools for studying ecological, evolutionary, and multi-scale processes within island communities.
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Development stage: A limited version is available. Further development is ongoing.
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The iBioGen publications are still in preparation. We plan to share them here, as soon as they are published. Our first publications are expected to be available by August 2020. In the meantime, we have selected a few relevant recent publications by our research teams that you may find interesting. Click on the images below to access the full text.
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