Bioinformatics for Microbial Genomics

Protocols for some of the 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 FilesSunbeam: How to Set-up / RunSourmash: alignment-free analysis of metagenomesCORRAL: detecting microbial eukaryotes in metagenomic dataMetaPhlAn4: taxomomic analysis of shotgun metagenomic data using clade-specific marker genesQIIME2: analysis of 16S dataQIIME2: analysis of data pulled from MicrobiomeDBHybrid assembly of bacterial genomesMicrobiomeDB: analysis of microbiome data online⬆️Upload to SRA/MicrobiomeDB