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microbial-succession

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Qasim-Hussain-Code / qiime2_microbial_succession_trajectory_amplicon_analysis

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QIIME 2-based pipeline for tracking microbial community succession, taxonomic profiling, and calculating chronological ecological diversity metrics.

bioinformatics computational-biology metagenomics microbiology microbiome biomarker-discovery microbial-ecology dada2 asv amplicon-sequencing microbiome-data qiime2 16s-rrna community-assembly ancom-bc microbial-succession ecological-diversity
  • Updated May 6, 2026
  • TeX

Qasim-Hussain-Code / moshpit_cocoa_fermentation_analysis

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A reproducible, shotgun metagenomics pipeline (MEGAHIT, MetaBAT 2, Sourmash, Kraken 2) characterizing the microbial ecology, taxonomic abundance, and genomic bins of cocoa fermentation.

metagenomics microbiome microbial-ecology qiime2 saccharomyces-cerevisiae metabolic-profiling moshpit lactobacillaceae lactic-acid-bacteria microbial-succession food-microbiology fermentation-ecology theobroma-cacao cocoa-fermentation acetic-acid-bacteria acetobacteraceae mag-recovery
  • Updated Jun 4, 2026
  • Python

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