Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp
Open accessAbstract
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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Adapter trimming and quality filtering were performed with fastp.
“Adapter trimming and quality filtering were performed with fastp (v0.23.4) [74].”
From Mechanical stiffness orchestrates distinct regulation of <scp>MRTFs</scp> and <scp>YAP</scp> / <scp>TAZ</scp> transcriptional cofactors in hepatocytes (2026) · cites this paper as [74]
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“23.2 [34] to remove adapters and filter low quality bases (Q 30) and short reads (length 150).”
InfluentialTorres‐Ortiz, B. S., Pérez‐Calixto, D., Carretero‐Ortega, J., Guzman‐López, A. G., Pinto‐Dueñas, D. C., Hernández‐Juárez, M., Jiménez‐Escobar, A., Rodríguez‐Hernández, A., Díaz‐Bello, B., Serna‐Márquez, N., et al. (2026) · The FEBS Journal · doi:10.1111/febs.70570
- Authors
- Chen, S.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Chen, Shifu
- ORCID
- Chen, Shifu
- Venue
- iMeta
- Publisher
- Wiley
- Published
- 2023-05
- Volume
- 2
- Issue
- 2
- Pages
- e107-e107
- ISSN
- 2770-596X (ISSN-L)
- 2770-5986
- PMC
- PMC10989850
- OpenAlex
- W4375863320
- Cited by
- 2,166
- References
- 2
- Citations by year
- 2026: 888 · 2025: 953 · 2024: 288 · 2023: 35 · 2022: 1 · 2020: 1
- FWCI
- 192.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- iMeta (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Science, Technology and Innovation Commission of Shenzhen Municipality (JSGG20180508152646606, JSGG20180703164202084, KQJSCX20180330124428928)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- fastp, adapter removal, read quality filtering, read deduplication, sequencing data quality control, bioinformatics software
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