MGX provides several analysis pipelines to align metagenome reads to reference genomes;
before these pipelines can be used, the corresponding reference genome has to be added
to the project. There are two possible ways to achieve this: The MGX repository hosts
published and annotated reference genomes obtained from the NCBI; in addition, users
may choose to upload a custom reference sequence in FASTA, GenBank or EMBL format, e.g.
a finished but unpublished genome not available from official sources.
To add a reference genome, right-click on the “Reference sequences” node within the
project view and select either “Add reference” to access the MGX repository or
“Upload EMBL/GenBank/FASTA reference” to provide an own sequence (2.31).
Once the import is complete, the reference genome is available for analysis and can be selected for the corresponding analysis pipelines which provide reference mapping, e.g. BowTie or FR-HIT.