The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
fastp 1.0: An ultra‐fast all‐round tool for FASTQ data quality control and preprocessing
Open accessAbstract
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.
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Citations
Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty560 · Cited by 29,721
Self-citationMultiQC: summarize analysis results for multiple tools and samples in a single report
Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw354 · Cited by 10,143
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Shen, W., Le, S., Li, Y., & Hu, F. (2016) · PLOS ONE · doi:10.1371/journal.pone.0163962 · Cited by 3,380
Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp
Chen, S. (2023) · iMeta · doi:10.1002/imt2.107 · Cited by 2,166
Self-citationBrown, J., Pirrung, M., & McCue, L. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx373 · Cited by 1,097
A survey of sequence alignment algorithms for next-generation sequencing
Li, H., & Homer, N. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq015 · Cited by 875
SeqKit2: A Swiss army knife for sequence and alignment processing
Shen, W., Sipos, B., & Zhao, L. (2024) · iMeta · doi:10.1002/imt2.191 · Cited by 484
Approximating Edit Distance Efficiently
Bar-Yossef, Z., Jayram, T. S., Krauthgamer, R., & Kumar, R. (2004) · Annual Symposium on Foundations of Computer Science · doi:10.1109/focs.2004.14 · Cited by 117
Cited by
Batista, C. S. P., Rivera, A., Alvarez Albarran, M. T., Rubio, M., Belen-Figas, I., Lopez-Querol, C., Miró, E., Navarro, F., & Sanchez-Reus, F. (2025) · Journal of Fungi · doi:10.3390/jof11110808 · Cited by 2
Metadata
- Authors
- Chen, S.
- Venue
- iMeta
- Publisher
- Wiley
- Published
- 2025-09-09
- Volume
- 4
- Issue
- 5
- Pages
- e70078-e70078
- ISSN
- 2770-596X (ISSN-L)
- 2770-5986
- OpenAlex
- W4414146635
- Cited by
- 258
- References
- 15
- FWCI
- 65.95
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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