QCatch

QCatch generates comprehensive, interactive HTML quality control reports for single-cell quantification results from alevin-fry or simpleaf, exporting processed results in H5AD format for downstream analysis.

Key Features:

• Cell Calling: Performs essential cell calling processing steps on single-cell quantification outputs.
• QC Visualizations: Generates detailed reports containing informative visualizations and statistics including unique molecular identifier (UMI) count distributions, sequencing saturation estimates, and splicing status information.
• H5AD Export: Exports processed results in a richly-annotated H5AD format file compatible with downstream single-cell data analysis tools.

Scientific Applications:

• Single-Cell RNA Sequencing Quality Control: Mitigates technical artifacts and ensures reliable downstream results through standardized QC reporting tailored for alevin-fry and simpleaf outputs.
• Single-Cell Data Preprocessing: Streamlines QC workflow integration into downstream single-cell analysis pipelines by processing quantification results and producing annotated data objects.

Methodology:

QCatch takes the output directory of alevin-fry or simpleaf as input, performs cell calling, and generates QC reports with UMI count distributions, sequencing saturation estimates, and splicing status information.