Outputs of MetaPUF

The outputs from the pipeline include the following files

• Protein sequence database/(s) : after running the pipeline, one folder named assemblies will be generated, in which a subfolder named databases will be created, all the generated protein sequence database/(s) are there.

• Report informing assemblies in each protein sequence db : these files can be found in the folder of assemblies

• search results from SearchGui: a folder naming as searchgui would be created, and the zipped preotin database searching results for each sample will be generated in this folder.

• Peptide/Protein reports from PeptideShaker : a folder naming as peptideshaker would be created, for each sample, three files will be generated by PeptideShaker tool in this folder, one mzid file, one peptide report file and one protein report file.

• Post-processing reports: a folder naming as Processed_Peptide_Reports would be created, containing csv files for each sample.

• GFF format report: in the Processed_Peptide_Reports file, a subfolder named as results would be careted, in which all the post-processed identification and semi-quantification results were transformed into a GFF file suitable for integrating into the MGnify website using a custom script, which mapped the identified proteins to their corresponding assembly.