Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp

Jun 13, 2024iMeta

Very fast single-step processing, quality checking, and duplicate removal of sequencing data using fastp

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Longevity & Aging on OpenScience ↗PubMed ↗DOI ↗OA ↗

Abstract

Fastp has been significantly improved to enhance the efficiency of FASTQ data preprocessing.

Fastp is designed to remove adapter contamination, filter low-quality reads, and correct errors in sequencing data.
Improvements include an enhanced duplication evaluation module and the addition of a new deduplication module.
The software has been continuously maintained and updated based on feedback from bioinformatics users.
The goal is to provide a faster, simpler, and more energy-efficient solution for sequencing data analysis.

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A large amount of sequencing data is generated and processed every day with the continuous evolution of sequencing technology and the expansion of sequencing applications. One consequence of such sequencing data explosion is the increasing cost and complexity of data processing. The preprocessing of FASTQ data, which means removing adapter contamination, filtering low-quality reads, and correcting wrongly represented bases, is an indispensable but resource intensive part of sequencing data analysis. Therefore, although a lot of software applications have been developed to solve this problem, bioinformatics scientists and engineers are still pursuing faster, simpler, and more energy-efficient software. Several years ago, the author developed fastp, which is an ultrafast all-in-one FASTQ data preprocessor with many modern features. This software has been approved by many bioinformatics users and has been continuously maintained and updated. Since the first publication on fastp, it has been greatly improved, making it even faster and more powerful. For instance, the duplication evaluation module has been improved, and a new deduplication module has been added. This study aimed to introduce the new features of fastp and demonstrate how it was designed and implemented.

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Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp

Abstract

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