Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Next-generation sequencing (NGS) data require preprocessing to remove adapter contamination and low-quality reads.
• Current preprocessing tools face performance limitations with increasing sequencing throughput and read lengths, creating a bottleneck in data analysis.

Purpose of the Study:

• To develop an extra-fast and accurate tool for adapter and quality trimming of NGS data.
• To address the unmet demand for efficient preprocessing solutions in high-throughput sequencing data analysis.

Main Methods:

• Ktrim was developed to perform adapter and quality trimming for both paired-end and single-end sequencing data.
• The tool supports common library preparation kit adapters and user-defined custom adapter sequences.
• Ktrim incorporates parallelization to accelerate the analysis process.

Main Results:

• Ktrim demonstrated significantly higher speed, being approximately 2-18 times faster than existing tools.
• The tool exhibited high accuracy in trimming adapter sequences and removing low-quality data across testing datasets.
• Ktrim effectively preprocesses short-read NGS data, enhancing downstream analysis.

Conclusions:

• Ktrim provides a valuable and efficient solution for the preprocessing of next-generation sequencing data.
• The tool's speed and accuracy make it suitable for handling large-scale, high-throughput sequencing datasets.
• Ktrim can help overcome performance bottlenecks in bioinformatics pipelines.