New and Updated Illumina Core Apps

Since our last app news in August and September, we’ve published more than 15 new and updated apps in BaseSpace! Let’s explore five of those:


The TruSight Tumor 15 app enables the analysis of samples prepared using the TruSight Tumor 15 library prep kit, and it offers a sample-to-answer solution for the detection of common somatic variants. Developed with key industry leaders, this panel focuses on genes most relevant for solid tumor analysis. The highly sensitive assay detects somatic mutations at 5% variant frequency and maximizes sample success from small amounts of FFPE samples. The app consumes these samples and then outputs reports detailing variants identified within the 15 genes of interest.

TST15ReportThe TruSeq Amplicon v2.0.0 app enables streamlined analysis of Illumina TruSeq Amplicon panels. Alignment is performed using the banded Smith-Waterman algorithm in the targeted regions. For variant calling, users can select from GATK 1.6, Starling, or Illumina-developed somatic variant caller.. With this update, the app now supports TruSeq Custom Amplicon Low Input analysis via the import of custom manifests.

The Amplicon DS v1.2.0 workflow enables analysis of samples generated using the TruSight Tumor 26 panel and dual pool (dual strand) TruSeq Custom Amplicon panels created in DesignStudio. The v1.2 update provides quicker turnaround time for analysis via multi-node anlaysis and the upload of custom manifests to enable analysis of custom panels.


The latest Isaac Whole Genome Sequencing v4.0.0 app has an enhanced version of the high-speed Isaac aligner, improved small variant, SV and CNV calling, and a new annotation module for more robust performance. This app performs read mapping and variant calling using open-source tools: the Isaac Genome Alignment Software and SNV, CNV and SV calling using Starling, Canvas, Manta, respectively.  This version of the Isaac app supports simultaneous analysis for up to 96 whole human genomes.

Picture4Finally, the latest Tumor Normal workflow contains an enhanced Isaac aligner, improved somatic variant calling, more robust annotation module, and multiple stability fixes. Additionally, the app provides the ability to begin analysis from FASTQs or BAM files generated by the Isaac WGS v4.0.0 app. This version of the Tumor Normal app enables concurrent analysis of up to 96 tumor/normal pairs.

Stay tuned for more updates on the latest apps available in the BaseSpace app store. Questions? Contact us at

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