Tapestri DNA, DNA + Protein Pipeline v3.4 27 March 2024

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  1. Seamless Integration of Genotype and Antibody based demultiplexing - Tapestri can now be used to multiplex data based on the differences in the genotype profiles or protein expressions across samples. This allows processing of multiple patient samples on a single Tapestri run as opposed to multiple Tapestri runs, one for each patient. The Tapestri Pipeline application can then be used to classify each cell into its original sample category.The new workflows are supported by choosing the “Run Mode” when staring a run. The following new workflows are enabled for TPDNA v3.4 and GE v1.1:
    1. DNA and DNA + Protein analysis with Genotype based demultiplexing supported by “Genotype Demultiplexing” run mode.
    2. DNA with Antibody based demultiplexing analysis supported by “Antibody Demultiplexing” run mode with DNA + Protein pipeline.
    3. GE DNA with automatic antibody based demultiplexing analysis supported by GE DNA+Protein pipeline.
  2. A new Bulk Merge pipeline that will ingest “Bulk” run mode tagged runs, and create the required genotype demultiplexing definition file by auto selecting appropriate germline variants suitable for uniquely identifying samples. Built in QC and UI input fields for sample naming allows pre-checking validity of sample combinations and generation of properly formatted file required for the genotype demultiplexing run mode.
  3. Reduced resource usage - With V3 chemistry and higher cell counts we were encountering failures due to resource exhaustion. Multiple steps within the pipeline were optimized to handle such high cell counts.
  4. Improved read trimming by use of cutadapt v4 - Cutadapt V4 has a hybrid algorithm for adapter alignment that results in a more intuitive and better trimming. This resulted in the following changes for the Tapestri data -
    1. Better read recovery for Protein.
    2. Non-informative reads from DNA are discarded at the first step. In case any DNA data is reprocessed a difference in cell counts is expected as this change results in update to the alignment step which in turn impacts the cell finder output.
  5. Adjusted over-sequencing QC checks - As more cells are expected with V3 chemistry, the over-sequencing check was updated to use 30,000 as expected cell count which should lead to lower QC failures.
  6. Improved Run reports - The reports are interactive which help user to hover over the plots to view the data. In addition warnings are added for certain metrics that help judge the quality of the run, for example, a coverage of <20 and >200 is flagged. For more details refer to this article.
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