Same tool, new features Meta-Omics Software for Community Analysis was previsously published as a pipeline for integrated metagenomics (MG) and metatranscriptomics (MT) data analysis. This new version includes the integration of a metaproteomics (MP) workflow for raw data analysis and binning for contigs resulting from assembly, and improvements on the assemly and annotation steps.

Integration of metaproteomics: Two workflows have been developed for the handling of MP spectra, both for label-free quantification and analysis. While this feature is not complete, it already allows for identification and quantification of proteins, using the results from the MG workflow as a reference database.

Integration of binning: contigs resulting from MG assembly can now be binned into contigs. In the next few weeks, CheckM will be integrated for quality check of bins.

Improvement of assembly: assembly was performed with one MG sample at a time. This made sense in the scenario where each MG sample came from a different microbial community, but if some samples come from the same community, it is advisable to perform assembly with all data together. It is now possible to perform 3 different assembly strategies in MOSCA: "unique" for performing assembly as previously, one assembly for MG sample; "all" for performing assembly with all MG data together, use it only if the samples come from very similar communities; "samples", which requires the "--mg-samples" to specify which samples go together for each assembly/annotation.

Improvement of annotation: domain annotation with PSI-BLAST and COG database is now possible within MOSCA. This type of annotation is focused on functional classification by identifying domains specific to metabolic and/or structural functions.