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.

Data in an intuitive graphical format

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.

MiSeq Reporter training

Learn how to analyze your data, and explore supported workflows.

Pre-installed databases and reference genomes

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).

Adding custom reference genomes to MiSeq Reporter

Learn how to add your own reference genome(s) of interest to MiSeq Reporter.

Computing requirements

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.

Download MiSeq Reporter or get support

See changes introduced in recent versions of MiSeq Reporter, and download the latest version. Or access MiSeq Reporter technical support information.

Download MiSeq Reporter
Access MiSeq Reporter support

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For every lab, everywhere

For every lab, everywhere

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For every lab, everywhere

MiSeq Reporter Software

For every lab, everywhere

Simple on-instrument data analysis

Data in an intuitive graphical format

MiSeq Reporter training

Pre-installed databases and reference genomes

For most workflows, a reference genome is required to perform alignment. MiSeq Reporter includes several pre-installed databases and genomes.

Adding custom reference genomes to MiSeq Reporter

Computing requirements

Download MiSeq Reporter or get support