microbiome topic
vsearch
Versatile open-source tool for microbiome analysis
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
swarm
A robust and fast clustering method for amplicon-based studies
DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
microbiomeMarker
R package for microbiome biomarker discovery
decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
microbiome
microbiome R package
qiita
Qiita - A multi-omics databasing effort
qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing