Improved barcode correction: We implemented a more stringent validation of barcode structure to reduce the % of reads incorrectly assigned to cells. A consequence of this is a marginal increase in the % of reads rejected (due to errors in both the barcodes in a read) and a marginal decrease in the number of cells found.
Runtime improvements: We made significant runtime improvements in several steps of the Pipeline. You receive the same results but much faster than before – up to 40 % faster for NovaSeq data.
Addition of barcodes to .loom files: The .loom files now contain the cell’s barcode information. This enables you to use the .loom files directly for copy number and loss of heterozygosity (LOH) analysis.
More informative error messages: Error handling has been improved to show appropriate messages to reduce the time spent on troubleshooting.