Fig. 1

HOME-BIO workflow. The pipeline accepts NGS data as input and then proceeds to perform the analysis according to the different steps comprised in the three modules. The Quality Control module (in orange) performs QCs of the reads, low-complexity reads removal, and host and contaminant sequencing reads filtering (indicated in the dark orange rectangle), generating as output quality reports and graphical charts (indicated in the light orange rectangle). The sequence reads maintained after this step are processed using the Metagenomic shotgun module (in green) and/or the Assembly de novo module (in blue). In the first case, the reads are processed by Kraken2 and Kaiju (indicated in the dark green rectangle), producing as output text tables and charts. The Assembly de novo module processes the sequences by assembling with SPAdes and annotating with Kraken2 (dark blue rectangle), generating as output text tables and charts. For both modules, a custom database (indicates in the grey box) is used