scarecrow

scarecrow recovers sequencing reads from single-cell combinatorial barcoding experiments by identifying barcode sequences with positional error correction ('jitter') to maximize read retention and improve downstream analysis.

Key Features:

• Jitter-aware barcode identification: Screens a subsample of reads to generate position-specific barcode profiles that flexibly identify barcode sequences while accounting for positional errors caused by technical artifacts during barcode incorporation or synthesis.
• Prioritized barcode matching: Prioritizes barcode matches to minimize nucleotide mismatches and the degree of jitter.
• Error correction: Uses initial profiles to extract and error correct barcode combinations in high throughput sequencing libraries.
• Standardized output: Generates output files using standardised sequence file formats.

Scientific Applications:

• Single-cell combinatorial barcoding data processing: Maximizes retention of sequencing reads from split-pool ligation protocols and other combinatorial barcoding technologies for single-cell nucleotide sequencing.
• Improved downstream single-cell analysis: Enables greater data recovery and improved downstream single-cell analyses by incorporating jitter into barcode error correction.

Methodology:

scarecrow screens a subsample of reads to generate position-specific barcode profiles, which are used to flexibly identify barcode sequences in each read while accounting for positional errors ('jitter'). Barcode matches are prioritized to minimize nucleotide mismatches and jitter, and initial profiles are subsequently used to extract and error correct barcode combinations in high throughput sequencing libraries.