scruff

scruff preprocesses single-cell RNA sequencing (scRNA-seq) data from CEL-Seq and CEL-Seq2 protocols by performing demultiplexing, cell barcode identification, UMI deconvolution and deduplication, alignment, and counting to produce quality metrics for downstream analysis.

Key Features:

• Demultiplexing and Alignment: Demultiplexes sequencing reads, aligns them to a reference genome, and counts reads mapped to genomic features.
• UMI Deduplication: Performs unique molecular identifier (UMI) deconvolution and deduplication to enable accurate molecule-level quantification.
• Quality Metrics and Visualization: Generates pre- and post-alignment quality metrics and visualizations, and produces read alignments annotated with UMI information at genomic coordinates to support isoform usage analysis.
• Compatibility and Integration: Supports visualization of quality metrics for sequence alignment files (e.g., Cell Ranger output) from 10X Genomics.
• Reproducibility and Reliability: Implements streamlined, reproducible preprocessing workflows for scRNA-seq data.

Scientific Applications:

• Transcriptional Profiling: Enables high-throughput quantification of transcriptional profiles at single-cell resolution.
• Isoform Usage Analysis: Facilitates examination of isoform usage differences through UMI-aware read alignment visualizations.
• Quality Control: Assesses and compares data integrity across samples or runs using comprehensive quality metrics.

Methodology:

Performs data demultiplexing, cell barcode identification, UMI deconvolution and deduplication, alignment to the genome, counting of reads mapped to genomic features, and reporting of quality metrics and visualizations for CEL-Seq and CEL-Seq2 scRNA-seq data.