Importing reference genomes

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addition, users may choose to upload a custom reference sequence in FASTA, GenBank or EMBL format, e.g. a finished but unpublished genome not available from official sources.

Figure 2.31: Reference sequences to be used as mapping targets may be imported from the global repository or uploaded in EMBL/GenBank/FASTA format.

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.