fastp: an ultra-fast all-in-one FASTQ preprocessor
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Summary
Fastp is developed as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features that can perform quality control, adapter trimming, quality filtering, per-read quality cutting, and many other operations with a single scan of the FastQ data.
- Type
- preprint
- Published
- 2018-03-01
- Cited by
- 24,965
- References
- 19
- Access
- Open access
- OpenAlex
- https://openalex.org/W2789720911
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:52196534
Keywords
Computer science, Trimming, Preprocessor, Python (programming language), Adapter (computing)
References
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- Detecting ultralow-frequency mutations by Duplex Sequencing
- Cutadapt removes adapter sequences from high-throughput sequencing reads
- The Sequence Alignment/Map format and SAMtools
- Trimmomatic: a flexible trimmer for Illumina sequence data
- SpeedSeq: Ultra-fast personal genome analysis and interpretation
- Fast gapped-read alignment with Bowtie 2
- Integrated digital error suppression for improved detection of circulating tumor DNA
- UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
- The Emerging Role of “Liquid Biopsies,” Circulating Tumor Cells, and Circulating Cell-Free Tumor DNA in Lung Cancer Diagnosis and Identification of Resistance Mutations
- AfterQC: automatic filtering, trimming, error removing and quality control for fastq data
- SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
- Fast and accurate short read alignment with Burrows–Wheeler transform
- Erratum to: Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data
- Theoretical and practical advances in genome halving
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- Draft Genome Sequences of Five Historical Bacillus anthracis Strains
- Rapid, robust plasmid verification by de novo assembly of short sequencing reads
- Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants
- Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1T
- Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice
- Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls
- Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil.
- Expression of laccase and ascorbate oxidase affects lignin composition in Arabidopsis thaliana stems
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
- Assembly-free and alignment-free sample identification using genome skims
- Machine Learning para caracterizar ARNs circulares en exosomas de sangre periférica como biomarcadores
- methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Accurate sequence variant genotyping in cattle using variation-aware genome graphs
- SIP: An Interchangeable Pipeline for scRNA-seq Data Processing
- Timing Polymerase Pausing with TV-PRO-seq
- Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)
- The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)
- A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle
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