Laboratory of Food Systems Biotechnology

RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere

q2-types-genomics

QIIME 2 types for genomics plugins.

advanced-comp-bio-tutorial

Hands-on demonstration of 16S rRNA gene sequence analysis for SysBio Advanced Block Course 2022

q2-assembly

QIIME 2 plugin for (meta)genome assembly.

HPV-multiOmics

Multi-Omics Predictive Modelling of Cervicovaginal Microenvironment

nf-ducken

Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.

q2-moshpit

MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking

q2-plugin-template

A skeleton for QIIME 2 plugins

q2-protein-pca

QIIME2 plugin for PCA analysis of protein sequence phylogeny.

uzh-microbiome-tutorial

db-benchmarks-2020

Database benchmarks using RESCRIPt

q2-coordinates

methods for geographic mapping of qiime2 artifact data or metadata

FermDB

ord-mishmash

q2-amr

q2-fondue-examples

Materials accompanying q2-fondue article.

cancer-microbiome-intervention-tutorial

JupyterBook for QIIME 2 FAES January 2022 workshop

DataVisualizationBook

JupyterBook on data visualization for Food Scientists.

Fermented-Food-Ontologies

Substrate-based fermented food ontologies

fgcz-metagenomics-workshop

q2-checkm

QIIME 2 plugin for assessing the quality of (meta)genomes using CheckM.

q2-exonerate

q2-pinocchio

q2-viromics

utilities

A collection of utilities used across repos.