fastp 1.0: An ultra‐fast all‐round tool for FASTQ data quality control and preprocessing
Shifu Chen
Abstract
Fastp has been recognized as one of the most popular FASTQ file preprocessors because of its powerful functions and extreme performance. As its first major update, fastp 1.0 will be formally presented in this paper, including its new features and the implementation principles behind it. Two other popular FASTQ preprocessors, Trimmomatic and Cutadapt, will be compared to demonstrate the great advantages of fastp in terms of simplicity, efficiency, and versatility. Some modules, such as the batch processing scripts, will be introduced on how to apply fastp to process FASTQ files efficiently. Additionally, some software design principles will be highlighted to showcase how to develop a successful bioinformatics software.
Topics & Concepts
Computer sciencePreprocessorProcess (computing)Data miningSoftwareQuality (philosophy)Control (management)Data pre-processingData processingData qualitySoftware engineeringDatabaseField (mathematics)Process controlWork (physics)Computational Physics and Python ApplicationsAlgorithms and Data CompressionHydrocarbon exploration and reservoir analysis