Amplicon sequence processing workflow using QIIME 2 and Snakemake
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Jul 27, 2026 - Python
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dada2
Here are 6 public repositories matching this topic...
Python-first amplicon denoising — byte-identical to R's DADA2
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Jul 31, 2026 - Python
Unified short-read workflow for multi-marker amplicon (16S, ITS, 18S, gyrB, rpoB) and shotgun taxonomic profiling. Snakemake, conda-based, reproducible.
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Aug 4, 2026 - Python
A reproducible nf-core/ampliseq pipeline characterizing antibiotic-mediated gut dysbiosis via paired-end 16S rRNA (V4) sequencing. Implements DADA2 exact sequence variant inference, SILVA-based taxonomic classification, and multivariate ecological ordination to quantify compositional perturbations in human fecal microbiomes.
nextflow bioinformatics-pipeline antibiotic-resistance microbiome-analysis human-microbiome microbial-ecology dada2 gut-microbiome amplicon-sequencing bacteriology bifidobacterium 16s-rrna nf-core dysbiosis microbial-diversity
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May 1, 2026 - Python
Harmonized cross-species 16S rRNA comparison of the gut microbiota in EAE mice and human multiple sclerosis
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Jul 13, 2026 - Python
ローカル LLM エージェントによる QIIME 2 マイクロバイオーム解析の完全自動化 — オフライン・APIキー不要・オープンソース
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Mar 25, 2026 - Python
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