Use of the new SPARC algorithm for Phylogeny creation
- What it does: SPARC (Single-cell Phylogeny And Reconstruction of Clones) is a computational method for inferring phylogenetic relationships from single-cell DNA sequencing data. The algorithm integrates somatic mutations, genome-wide loss of heterozygosity (LoH), and copy number variations (CNVs) in a single phylogeny. It replaces the COMPASS phylogeny tool which was used in the previous version of the software.
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Key Highlights:
- Better phylogeny trees integrating all possible events.
- Higher cell recovery for all the samples as the Ambiguous cell population created during merging CNV clones with Compass called clones decreases.
- Due to the updated DNA+Protein merge logic retaining more cells, processing the FASTQ again may result in slightly different variants and phylogeny
Integration of the latest variant filtering algorithm
- Updated variant filters developed as part of Clonal Insights v1 are now added to the MM pipeline which will help reduce the false positive and negative variants in the output.
Better CNV clone calling
- The CNV clones will be updated as part of this release due to the enhancements to the LoH finder and the CNV clone calling algorithms.
Updated VDJ clonotype data and visualization
- VDJ reference was updated to the latest version and several new visualizations are added to the reports.
Addition of cell clustering to Protein UMAP/Protein expression correlation plots
- Protein data is now clustered using unsupervised clustering methods and all the visualizations now show data based on these clusters in the report.