Protocols for some of routine computational tasks used in our lab are outlined below. If you’re looking for online tools for analyzing your own data, or published data, be sure to check out our MicrobiomeDB resource.
Checking the quality of raw reads
Analysis of 16S data using QIIME2
Alignment-free analysis of raw reads using Sourmash
Hybrid assembly of bacterial genomes
Analysis of microbiome data on microbiomeDB
Analysis of shotgun metagenomic data using metaphlan2
Upload to SRA/MicrobiomeDB