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Augustin Žídek
@Augustin-Zidek
Jeremy Wohlwend
@jwohlwend
Sarah K Hu
@shu251
Chatterjee Lab
@programmablebio
Dr. Hafiz Saqib Ali
@HafizSaqibAli
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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.
A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.
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