Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Next-generation sequencing (NGS) generates vast amounts of data requiring efficient preprocessing.
• Adapter sequences and low-quality reads can compromise downstream analysis accuracy.
• Accurate identification and demultiplexing of sequencing reads are essential for sample tracking.

Purpose of the Study:

• To develop a fast and lightweight software tool for preprocessing NGS data.
• To enable efficient trimming of adapter sequences and low-quality regions from sequencing reads.
• To provide reliable identification of barcodes for sample assignment.

Main Methods:

• Utilizes a modified Myers's bit-vector dynamic programming algorithm.
• Implements adapter trimming from both or either end of reads.
• Incorporates indel handling for adapters and barcodes.
• Designed for high-throughput sequencing data.

Main Results:

• Btrim achieves fast trimming speeds, processing 30 million reads in approximately one minute.
• The software exhibits a small memory footprint.
• Demonstrates reliable identification of barcodes and assignment of reads to original samples.
• Effectively removes low-quality regions and adapter sequences.

Conclusions:

• Btrim is a versatile and efficient tool for essential NGS data preprocessing.
• Its speed, low memory usage, and accuracy make it suitable for ultra-high-throughput sequencing.
• Serves as a foundational step for various next-generation sequence analysis pipelines.