posDemux

posDemux demultiplexes and filters sequencing reads containing combinatorial barcodes such as those used in PETRI-seq and SPLiT-seq by using segment positions to extract and compare barcodes against a reference whitelist.

Key Features:

• Positional barcode extraction: The demultiplexer algorithm uses the position of segments to extract barcodes from combinatorial barcode structures.
• Whitelist comparison: Extracted barcodes are compared against a reference whitelist for accurate demultiplexing.
• Combinatorial barcode support: Handles reads with combinatorial barcodes as used in PETRI-seq and SPLiT-seq protocols.
• Interactive cutoff selection: A Shiny application enables interactive selection of cutoffs for determining which barcode combinations to retain.

Scientific Applications:

• PETRI-seq analysis: Demultiplexing and filtering of PETRI-seq combinatorial barcode reads.
• SPLiT-seq analysis: Demultiplexing and filtering of SPLiT-seq combinatorial barcode reads.

Methodology:

The demultiplexer algorithm uses the position of the segments to extract and compare the barcodes with the reference whitelist.