QuAdTrim

QuAdTrim performs quality control and adapter trimming of high-throughput sequencing reads to remove low-quality bases and platform-specific homopolymer G artifacts for downstream analyses.

Key Features:

• Quality-based trimming: Removes or trims poor-quality reads and low-quality bases from HTS datasets to improve input data quality.
• Adapter trimming: Detects and trims sequencing adapters from reads to prevent adapter-derived artifacts in downstream analyses.
• Homopolymer G correction: Removes homopolymer G runs from the 3’ ends of reads to correct artifacts common on NovaSeq, NextSeq, and iSeq100 platforms.
• High speed: Executes quality-control operations up to 57 times faster than other commonly used HTS quality control programs.
• Low memory usage: Operates using less than 0.06% of the memory typically consumed by similar programs.

Scientific Applications:

• Genome assembly: Produces higher-quality input reads to reduce assembly errors and improve contiguity.
• Variant calling: Reduces false positives and improves confidence in SNP and indel detection by removing low-quality and artifactual bases.
• Transcriptome profiling: Improves accuracy of expression quantification by eliminating adapter contamination and platform-specific read artifacts.

Methodology:

Performs quality-based read trimming, adapter detection and trimming, and targeted removal of 3’ homopolymer Gs using a streamlined algorithm optimized for speed and minimal memory usage.