I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?

Galaxy has a tool named Sixgill that can be used to convert the nucleic acid sequences to ‘metapeptide’ sequences. There are other options available within Galaxy such as the GalaxyGraph approach and Metagenome Binning, Assembly and Annotation Workflow. Please contact us, if you need assistance.