MOSCA (portuguese for fly) is a pipeline designed for performing metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP) integrated data analysis, in a mostly local and fully automated workflow. Metagenomics is used to build a reference database for MT and MP, beginning with preprocessing of data for removal of Illumina adapters and lower quality regions, folowed by assembly of reads into contigs, gene calling on the contigs and homology-based and domain-based annotation of identified proteins, using the UniProt and COG databases, respectively. If available, MT reads are then aligned to the ORFs for gene expression quantification, and MP spectra are submitted for Peptide-to-Spectrum matching, with the annotated ORFs as reference database. Final steps include differential expression analysis for both MT and MP, and metabolic pathways analysis through KEGG Pathways.