fastp: an ultra-fast all-in-one FASTQ preprocessor.

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• FASTQ file quality control and preprocessing are critical for accurate downstream genomic data analysis.
• Traditional tools often require multiple steps and lack efficiency due to high-level programming and limited multi-threading.
• Sequential data processing and repeated I/O operations slow down preprocessing pipelines.

Purpose of the Study:

• To develop an ultra-fast and efficient preprocessor for FASTQ files.
• To integrate quality control, adapter trimming, and filtering into a single, streamlined operation.
• To improve the speed and I/O efficiency of genomic data preprocessing.

Main Methods:

• Developed fastp, a novel FASTQ preprocessor implemented in C++ with multi-threading support.
• Integrated multiple preprocessing operations including quality control, adapter trimming, and quality filtering.
• Performed a single scan of FASTQ data for all operations.

Main Results:

• Fastp achieves ultra-fast performance, being 2-5 times faster than existing tools like Trimmomatic and Cutadapt.
• The tool integrates multiple operations, including quality control, adapter trimming, and filtering, in a single pass.
• Demonstrated significant improvements in speed and I/O efficiency for FASTQ data preprocessing.

Conclusions:

• Fastp offers a highly efficient and integrated solution for FASTQ file preprocessing.
• The tool significantly accelerates bioinformatics analyses by reducing processing time and resource usage.
• Fastp is available as open-source software, facilitating its adoption in research.