CellBarcode

CellBarcode performs cellular DNA barcode extraction and filtering from bulk or single-cell sequencing data using a variety of filtering strategies.

Key Features:

• Versatile barcode handling: Handles all kinds of DNA barcodes within a single sequencing read that have a pattern matchable by regular expression, including barcodes with flexible lengths and with or without UMI (unique molecular identifier).
• Multiple filtering strategies: Implements a variety of filtering strategies for barcode extraction and filtering.
• Barcode simulation: CellBarcodeSim, a companion barcode simulation kit, enables investigation of technical and biological factors influencing barcode identification.
• Amplicon data pre-processing: Can be used for pre-processing amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

Scientific Applications:

• Cellular barcode analysis: Identifies true DNA cellular barcodes among polymerase chain reaction and sequencing errors.
• CRISPR gRNA screening: Pre-processes amplicon data for CRISPR guide RNA screening experiments.
• Immune repertoire sequencing: Pre-processes immune repertoire sequencing data.
• Metagenome analysis: Pre-processes metagenome sequencing data.
• Barcode identification optimization: Provides a decision tree for optimizing barcode identification for different barcode settings based on simulation and biological data.

Methodology:

Barcode extraction uses regular expression pattern matching for barcodes within single sequencing reads. Filtering strategies are applied to distinguish true barcodes from PCR and sequencing errors. CellBarcodeSim simulates barcodes to evaluate technical and biological factors affecting barcode detection.