MiSeq Reporter version 2.4 Now Available in BaseSpace

With the latest update of BaseSpace, we have updated the MiSeq Reporter (MSR) Workflows to v2.4! This means all users streaming MiSeq data to BaseSpace with automatic analysis launch will now have the latest and greatest features incorporated since the release of MSR v2.2 in BaseSpace. MSR v2.4 in BaseSpace will also provide consistent results with MSR local v2.4, released in March, 2014.

For full details on the MSR v2.4 release in BaseSpace, please see the Customer Release Notes.

New platform level features

  • gVCF file output for TruSeq Amplicon, Enrichment, and PCR Amplicon workflows. The gVCF files provide data at all genomic coordinates assayed, regardless of the variant status, and show the reference allele if no variant is found. For more information on gVCF files, please see the following link: https://sites.google.com/site/gvcftools/home/about-gvcf
  • BAM and VCF/gVCF files are now stamped with a header containing algorithm versions and parameter settings to easily track your analysis details. msr vcf stamp
  • Updated the Starling variant caller to v2.0.3 for use with TruSeq Amplicon, Resequencing, and PCR Amplicon workflows. The default variant caller for these workflows remains GATK v1.6.
  • Enabled StitchedReads in the TruSeq Amplicon and GenerateFASTQ workflows. Read stitching allows construction of a single, longer read from two overlapping, shorter paired reads. For more information on Stitched Reads, please see the Customer Release Notes.

Highlights for specific workflows

  • The 16S Metagenomics workflow now allows species-level identification (previous versions stopped at genus-level). To classify down the species level, add the sample sheet setting described in the Customer Release Notes, or use Illumina Experiment Manager v1.7 to build your sample sheet. We also added a new, interactive HTML output report to dive deep into your 16S data. Lastly, the classification algorithm has been updated to provide faster results.
    16s Metagenomics
  • The Enrichment workflow now allows users to specify padding values in the sample sheet. Please see the Customer Release Notes for additional details.

If you have any older runs that you want to push through these new workflows, please contact support through the “Contact Us” button on the site.


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