Journal
BIOINFORMATICS
Volume 34, Issue 17, Pages 884-890Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty560
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Funding
- Special Funds for Future Industries of Shenzhen [JSGG20160229123927512]
- National Science Foundation of China [61472411]
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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 Cthornthorn 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.
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