Assessing reproducibility of metagenomics studies and diversity of public transport systems microbiome profiles of New York, Boston and Sacramento cities

Raw fastq files were analyzed with FastQC (Andrews et al., 2010) and results were aggregated using MultiQC (Ewels et al., 2016), we repeated this procedure each time we applied any modification to the data to check the impact of the processing. All the data was processed with AfterQC (Chen et al., 2017) tool, which does automatic filtering, trimming, error removing and quality Control for fastq data. Nevetheless, Boston and NY datasets required additional adapters trimming, so we used Trim Galore (Krueger, 2015) to remove Nextera adapters, optionally we used Prinseq (Schmieder et al., 2011) just to filter reads by length (we eliminated reads < 70 bp).