TriageTools

TriageTools partitions raw high-throughput sequencing (HTS) datasets to extract FASTQ reads likely to map to predefined genomic regions for targeted analysis of genes and pathways.

Key Features:

• Data Partitioning: Partitions raw sequencing data (FASTQ reads) to extract subsets corresponding to predefined regions of interest.
• Read Extraction Method: Employs a method for extracting reads likely to map onto targeted genomic regions to avoid processing irrelevant reads.
• Performance: Achieves reported speedup factors ranging from 2.6 to 96 depending on settings and sample types.
• Sample Types: Applicable to both DNA and RNA sequencing samples.
• Resource Optimization: Reduces computation time and disk space by focusing analyses on reads relevant to specified genes or pathways.

Scientific Applications:

• Targeted genomic analyses: Enables partitioning of datasets to include only reads relevant to specific genes or pathways.
• Gene expression: Supports focused gene expression studies by extracting transcript-specific reads.
• Variant calling: Facilitates variant calling on predefined genomic regions by supplying targeted read subsets.
• Pathway analysis: Allows pathway-level investigations by extracting reads mapping to pathway-associated genes.

Methodology:

Identifies and extracts sequencing reads likely to map onto predefined regions of interest using a selective extraction process facilitated by algorithms that maximize relevance while minimizing unnecessary data processing.