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.
FastQC and MultiQC: checking quality of raw reads
fastq_screen: QC analysis of sequencing data
Humann: How to Set up / Run on Paired Files
Sunbeam: How to Set-up / Run
Sourmash: alignment-free analysis of metagenomes
CORRAL: detecting microbial eukaryotes in metagenomic data
MetaPhlAn4: taxomomic analysis of shotgun metagenomic data using clade-specific marker genes
QIIME2: analysis of 16S data
QIIME2: analysis of data pulled from MicrobiomeDB
Hybrid assembly of bacterial genomes
MicrobiomeDB: analysis of microbiome data online
Upload to SRA/MicrobiomeDB