- 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.
- Change in Cutadapt version: The Pipeline now uses Cutadapt v2.3.
- 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.