Instructions for references

1) Create a FASTA file called “consensus.fasta”; alternatively, you can alter your “init.sh” for the module and use a different filename by setting the “REF_SET” variable to your default reference library. You can override your module default reference library at the config file level as well.

2) The FASTA file should contain one sequence per each genome lineage and/or gene segment. The header should contain the name of gene segment and/or type/lineage/subtype. Spaces are not allowed. The recommended solution is to build an alignment for each and take the consensus sequence without using mixed base calls (plurality consensus).

3) Create a text file describing the data for others to reference.