How to properly format and use a custom reference genome in MiSeq Reporter
MiSeq instruments with MiSeq Control Software (MCS 2.6) or earlier include several pre-installed reference genomes that are used during the alignment and variant calling steps of many MiSeq Reporter analysis workflows, which can also utilize user-added custom reference genomes. A custom reference genome file must be properly formatted and added to the MiSeq Reporter and Illumina Experiment Manager (IEM) Genome repositories so that it can be used for analysis in MiSeq Reporter. Custom reference genomes cannot be used for analysis in BaseSpace.
The file must be in FASTA format using the \.fa extension, not the \.fasta extension.
Use a text editor such as Notepad or TextEdit, or a source code editor like Notepad++, to edit your file.
Sequence identifiers are limited to 24 characters and can only contain letters, numbers, hyphens, and underscores. All other characters, including blank spaces, are not allowed in the sequence identifiers.