TrieDedup

TrieDedup removes PCR duplicates from high-throughput sequencing reads using a trie-based algorithm that preserves accuracy when ambiguous bases ('N's) are present.

Key Features:

• Efficient Deduplication: Achieves up to 270-fold faster deduplication of raw sequences compared to traditional pairwise comparison methods.
• Handling Ambiguous Bases: Incorporates ambiguous bases ('N's) into the deduplication logic to accurately identify and remove PCR duplicates from low-quality reads.
• Memory Optimization: Reduces memory usage by approximately 20% via a restrictedDict implementation in Python.
• Versatile Applications: Supports PCR deduplication, barcode and Unique Molecular Identifier (UMI) assignment, and repertoire diversity analysis.

Scientific Applications:

• PCR Duplicate Removal: Removes PCR duplicates from high-throughput sequencing datasets to improve data accuracy.
• Barcode and UMI Assignment: Enables barcode and Unique Molecular Identifier (UMI) assignment workflows for large-scale sequencing analyses.
• Repertoire Diversity Analysis: Facilitates repertoire diversity analysis for studies of genetic variability and function.

Methodology:

Sequences are stored and compared in a trie (prefix tree) that accounts for ambiguous bases ('N'); memory is optimized via a restrictedDict implemented in Python.