Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Profiler for metagenomics based on NGLess
Quantitative metagenomic alignment and taxonomic exact-matching
Docker and Singular container definition files, as used by the MbiomeCore at JAX-GM
metagenome simulation for targeted and reduced-representation sequencing
Use one command to perform genome-centric metagenomics using state-of-the-art methods
A flexible and modular pipeline for metagenomic analysis.
Tutorials on microbiome analysis using the Quantitative Insights Into Microbial Ecology (QIIME) platform
The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions
Shotgun metagenomics pipeline to process raw Illumina paired-end reads into usable microbiome data, suitable for Phyloseq postprocessing.
16S Microbiome Analysis Pipeline. This version written in Nextflow.
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