SG2: TerminalTrace (v1.0.0) High-speed terminal sequence motif analyzer for FASTQ data. Developed by DR Saminathan Sivaprakasham Murugesan Sumathi Genomics Co Ltd (Thailand) | Saminathan Industries Pte Ltd (Singapore)

Overview SG2: TerminalTrace is a specialized bioinformatics engine designed to characterize the fragmentation patterns of DNA. While its predecessor, SG1, focuses on high-performance genetic circuit design via CUDA, SG2 provides a streamlined, memory-efficient approach to analyzing terminal sequence motifs. Terminal motifs (the sequence of bases at the ends of DNA fragments) are essential biomarkers in liquid biopsy and cell-free DNA (cfDNA) research. These motifs reflect the enzymatic cleavage processes (e.g., DNASE1L3 activity) that occur during apoptosis and necrosis, providing insights into tissue-of-origin and disease states.

Key Features Streaming Architecture: Uses a generator-based approach to ensure a low memory footprint (<100MB) even when processing multi-gigabyte FASTQ/GZ files. Dual-End Tracking: Independently analyzes the 5' (Leading) and 3' (Trailing) termini to account for library preparation biases. Quality Gating: Integrates Phred quality score filtering (default Q20) to ensure that motif calls are derived from high-confidence sequencing data. Flexible k-mer Analysis: User-definable motif lengths ($k$) to capture everything from single-nucleotide ends to complex 4-mer or 6-mer patterns.

Technical Specifications

1. The Algorithm SG2 scans the boundary bases of every valid sequencing read. It converts sequences to a uniform uppercase format and handles ambiguous bases (N), ensuring a complete representation of the raw data.
2. Quality Control The tool calculates the average Phred quality score ($Q$) for each read. Reads falling below the user-defined threshold are discarded:

$$Q = -10 \log_{10}(P)$$ (Where $P$ is the probability of an incorrect base call). 3. Performance The script is optimized for I/O efficiency, utilizing buffered reading for compressed Gzip streams. It operates with $O(n)$ time complexity, where $n$ is the total number of reads.

SG2: TerminalTrace (v1.0.0)

High-speed terminal sequence motif analyzer for FASTQ data.

Developed by DR Saminathan Sivaprakasham Murugesan Sumathi Genomics Co Ltd (Thailand) | Saminathan Industries Pte Ltd (Singapore)

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Overview

SG2: TerminalTrace is a specialized bioinformatics engine designed to characterize the fragmentation patterns of DNA. While its predecessor, SG1, focuses on high-performance genetic circuit design via CUDA, SG2 provides a streamlined, memory-efficient approach to analyzing terminal sequence motifs.

Terminal motifs (the sequence of bases at the ends of DNA fragments) are essential biomarkers in liquid biopsy and cell-free DNA (cfDNA) research. These motifs reflect enzymatic cleavage processes, providing insights into tissue-of-origin and disease states.

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Key Features

• Streaming Architecture: Low memory footprint (<100MB) even for large datasets.
• Dual-End Tracking: Analyzes 5' and 3' termini independently.
• Quality Gating: Built-in Phred quality score filtering (Default Q20).
• Flexible k-mer Analysis: User-definable motif lengths.

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Installation

# Clone the repository
git clone [https://github.com/sumathigenomics/sg2_terminaltrace.git](https://github.com/sumathigenomics/sg2_terminaltrace.git)
cd sg2_terminaltrace

# Install dependencies
pip install biopython