MiSeq Reporter software performs secondary data analysis, and is pre-installed on MiSeq sequencers. It processes base calls generated on-instrument during the sequencing run by Real Time Analysis software.
Upon completion of real-time analysis, MiSeq Reporter launches automatically. It produces information about alignment, structural variants, and contig assemblies for each genome and sample. It performs analysis based on the workflow specified in the sample sheet.
MiSeq Reporter provides data from primary and secondary analysis, as well as quality and coverage information about each sample, in a simple and intuitive graphical format.
For most workflows, a reference genome is required to perform alignment. MiSeq Reporter includes several pre-installed databases and genomes.
Databases: miRbase for human, dbSNP for human, and refGene for human
Genomes: Arabidopsis thaliana, cow (Bos taurus), E. coli strain DH10b, human (Homo sapiens) build hg19, mouse (Mus musculus), rat (Rattus norvegicus), Staphylococcus aureus, and yeast (Saccharomyces cerevisiae).
You can also upload your own reference genomes in fasta format (*.fasta or *.fa).
MiSeq Reporter runs as a Windows service and is viewed through a web browser. If you'd like to analyze your data while the MiSeq System is performing a subsequent run, you can install another copy of the software on a separate computer.
See the MiSeq Reporter Computing Requirements support page for additional requirements.