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

Abstract

Motivation: Quality control (QC) and preprocessing of FASTQ files are necessary steps to provide clean data for downstream analysis. Traditionally, for each operation, such as QC, adapter trimming and quality filtering, a different tool is used. These tools are usually not fast enough since they are mostly developed in high-level programming languages like Python and Java, and provide limited multi-threading support. Also, the necessity to read and load data for multiple times makes the preprocessing slow and I/O inefficient. Results: We developed fastp as an ultra-fast FASTQ preprocessor with most useful QC and data filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality cutting and lots of other operations within a single scan of the FASTQ data. It also supports unique molecular identifier (UMI) preprocessing, poly tail trimming, output splitting, and base correction for paired-end data. It can automatically detect the adapters for both single-end and paired-end 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 like Trimmomatic or Cutadapt, in spite of that fastp performs much more operations than the latter ones. Availability and Implementation:The open-source code and corresponding instructions are available at: https://github.com/OpenGene/fastp Contact: chen@haplox.com

Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019

“…Quality control processes included adapter trimming, low quality reads removal, short reads removal by fastp (-l 70, -x, --cut-tail, --cut_tail_mean_quality 20, version: 0.20.0) [24], low complexity reads removal by Komplexity (-F, -k 8, -t 0.2, version: Nov 2019) [25], host removal by bmtagger (ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger) [26,27], and ribosomal reads removal by SortMeRNA (version:2.1b) [28].…”

Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs

“…The sequenced reads were demultiplexed using bcl2fastq (https://github.com/brwnj/bcl2fastq.) and the adapters were removed using fastp version 0.19.5 (Chen et al, 2018) (https://github.com/OpenGene/fastp). The reads were then assembled using MEGAHIT version 1.1.4 (Li et al, 2016), with default settings.…”

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

“…was shotgun-sequenced on the same platform by Novogene Co., Ltd. (Beijing, China) used for 150 bp paired-end reads. Raw paired-end reads were filtered using fastp v.0.13.2 (Chen et al, 2018) with the following parameters: -q 5 -u 50 -l 50 -n 15. Default values were used for the other settings.…”