MIntO: a Modular and Scalable Pipeline for Microbiome Metagenomic and Metatranscriptomic Meta-omics Data Integration

To illustrate the use of MIntO, a set of 91 human fecal metagenomes from the Inflammatory Bowel Disease Multi’omics Database was selected (IBDMDB). We selected six participants diagnosed as non-IBD (P6018 (nIBD1), M2072 (nIBD2)); Crohn’s disease (H4006 (CD1) and H4020 (CD2)); and ulcerative colitis (H4019 (UC1) and H4035 (UC2)) that were followed for one year each. Here, we present the results from the genome-based assembly-dependent mode, where we used 91 metagenomic high-quality reads to recover 163 high-quality MAGs, which constituted a set of non-redundant genomes.