Bioinformatics· 2018Q1
fastp: an ultra-fast all-in-one FASTQ preprocessor
- 30,201citations
- Q1SCImago
- 2018year
Short summary
A new C++-based tool called fastp has been developed to perform quality control and preprocessing of FASTQ files, integrating multiple operations into a single scan.
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Key points
- fastp integrates quality control, adapter trimming, and filtering into a single FASTQ data scan.
- Developed in C++ with multi-threading for enhanced speed.
- Achieves 2-5x faster performance compared to tools like Trimmomatic and Cutadapt.
- Reduces I/O inefficiency by reading data only once.
AI-generated from the title and abstract; the full text is not read.
Abstract
Motivation: Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results: We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation: The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
The authors' abstract, as published at the source. Bioinformatics, 2018 · DOI ↗
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Field: Hardware and Architecture
Hardware and ArchitectureComputer Science