A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
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microbiome analysis of ant colonies
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
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Natural Resources SILVA Application
QIIME 2 pipeline for 16S and ITS amplicon analysis of soil microbiome perturbation under antibiotic stress gradients (PRJEB95045).
Reproducible 16S/18S metabarcoding pipeline (VSEARCH + Wang-style k-mer classifier). Benchmarked against mothur and QIIME 2 — ECCB 2026.
microbiome analysis of ant colonies
Workflow and R scripts for Giongo et al. (2024)
QIIME 2 による 16S rRNA アンプリコン解析を学ぶための包括的日本語マニュアル — 各手法のメリット・デメリットを解説
Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.
Next Generation Phylogenetic Microbiome Analysis Framework
Workflow and R scripts for Braun-Kiewnick et al. (2024)
16S rRNA microbiome analysis of Lōʻihi seamount samples using mothur, SILVA alignment, OTU clustering, taxonomy, and rarefaction.
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