The cassava genome hub
Jan 3, 2018·
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0 min read
Anestis Gkanogiannis
Dereeper Alexis
Szurek Boris
Zarate Carlos
López Camilo
Becerra López-Lavalle Luis Agusto
Ruiz Manuel
Abstract
This portal (www.cassavagenome.org) is an integrative genome information system that allows centralized access to genomics and genetics data, and analytical tools to facilitate translational and applied research in cassava. As we did previously for the Banana Genome Hub (Droc et al. 2013) and the Coffee Genome Hub (Dereeper et al. 2015), we opted for GMOD components that are open source, modular, portable and benefiting from a large community support in which we have been involved. We also plugged numerous in-house tools developed by the South Green bioinformatics platform () such as SNiPlay (Dereeper et al. 2015) and Gigwa (Sempéré et al. 2016) for the exploration of the huge amount of genomic variations available in Cassava, notably through diversity or GWAS studies, DiffExDB to access RNA-Seq and differential expression data, as well as new components dedicated to interactions with Cassava pathogens.
Type
Publication
In Proceedings Plant and Animal Genome XXVI Conference, 2018 PAG, San Diego
Authors
Senior AI/ML and genomics practitioner
Senior AI/ML and genomics practitioner with ~15 years building open-source, production-grade tools for large-scale biological data. Maintainer of multiple Bioconductor packages (fastreeR, metabinR, jvecfor), and author of agentic, LLM-driven tooling that runs reproducible bioinformatics workflows from natural-language requests.
Broad multi-omics background spanning genome assembly and annotation, population genomics, large-scale NGS and functional-genomics analysis, and metagenomics, backed by reproducible HPC software and end-to-end program leadership. Currently focused on bringing modern AI — embeddings, deep learning, and LLM-based agents — to making complex omics datasets faster and easier to interrogate.