Skip to search formSkip to main contentSkip to account menu
DOI:10.1093/bioinformatics/bty560 - Corpus ID: 52196534
@article{Chen2018fastpAU, title={fastp: an ultra-fast all-in-one FASTQ preprocessor}, author={Shifu Chen and Yanqing Zhou and Yaru Chen and Jia Gu}, journal={Bioinformatics}, year={2018}, volume={34}, pages={i884 - i890}, url={https://api.semanticscholar.org/CorpusID:52196534}}
- Shifu Chen, Yanqing Zhou, Jia Gu
- Published in bioRxiv 1 March 2018
- Computer Science
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.
10,599 Citations
1,379
562
2,831
8
Topics
Fastp (opens in a new tab)Adapter Trimming (opens in a new tab)SOAPnuke (opens in a new tab)AfterQC (opens in a new tab)Cutadapt (opens in a new tab)Adapter Trimmer (opens in a new tab)FastQC (opens in a new tab)Adapter Contamination (opens in a new tab)Base Correction (opens in a new tab)Adapter Sequences (opens in a new tab)
10,599 Citations
- Jiacheng ChuanAiguo ZhouL. HaleMiao HeXiang Li
- 2021
Computer Science, Biology
bioRxiv
Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (O(n) time with O(1) space) that can be used in a broad range of short-sequence matching applications.
- Kun Sun
- 2020
Computer Science, Biology
Bioinform.
Ktrim was ∼2-18 times faster than current tools and also showed high accuracy when applied on the testing datasets and could serve as a valuable and efficient tool for short-read NGS data preprocessing.
- 24
- PDF
- Hao ZhangHonglei Song Weiguo Liu
- 2023
Computer Science, Biology
IEEE/ACM Transactions on Computational Biology…
RabbitFX is a fast, efficient, and easy-to-use framework for processing biological sequencing data on modern multi-core platforms that can efficiently read FASTA and FASTQ files by combining a lightweight parsing method by means of an optimized formatting implementation.
- 2
- Highly Influenced
- Lifeng YanZekun Yin Weiguo Liu
- 2023
Computer Science, Biology
Methods
- Xiaoshuang LiuZhenhe YanChao WuYang YangXiaoming LiGuangxin Zhang
- 2019
Computer Science
BMC Bioinformatics
FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes and is an all-in-one software that is convenient for bulk data analysis.
- 13
- PDF
- Lifeng YanZekun Yin Weiguo Liu
- 2022
Computer Science
2022 IEEE International Conference on…
RabbitQCPlus is an ultra-efficient quality control tool for modern multi-core systems that uses vectorization, memory copy reduction, parallel (de)compression, and optimized data structures to achieve substantial performance gains.
- Andrea TelatinP. FariselliG. Birolo
- 2021
Computer Science, Biology
Bioengineering
A suite of tools, called SeqFu (Sequence Fastx utilities), that provides a broad range of commands to perform both common and specialist operations with ease and is designed to be easily implemented in high-performance analytical pipelines.
- 25 [PDF]
- Behnam KhaleghiTianqi Zhang Tajana Rosing
- 2022
Computer Science, Biology
2022 IEEE Biomedical Circuits and Systems…
This work proposes the first FPGA-based framework dubbed FAST to accelerate the stages that deal with sequence trimming, in particular adapter and primer removal, which supports a comprehensive set of functionalities and is convenient to use by operating on standard genomics data formats.
- 1
- Highly Influenced
- Ting-Hsuan WangCheng-Ching HuangJui-Hung Hung
- 2021
Computer Science, Biology
Bioinform.
A set of fast and accurate adapter detection and trimming algorithms that entail no a priori adapter sequences are introduced that are particularly useful in meta-analyses of a large batch of datasets and can be incorporated in any sequence analysis pipelines in all scales.
- 3
- Guilherme de Sena BrandineAndrew D. Smith
- 2019
Computer Science, Biology
F1000Research
Falco is presented, an emulation of the popular FastQC tool that runs on average three times faster while generating equivalent results and requires less memory to run and provides more flexible visualization of HTML reports.
- 50 [PDF]
...
...
20 References
- Yuxin ChenYongsheng Chen Qiang Chen
- 2018
Computer Science, Biology
GigaScience
SOAPnuke is demonstrated as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework that enables large scalability to distribute all the processing works to an entire compute cluster.
- 1,163 [PDF]
- Anthony M. BolgerM. LohseB. Usadel
- 2014
Computer Science, Biology
Bioinform.
Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
- 42,425 [PDF]
- Shifu ChenTanxiao HuangYanqing ZhouYue HanMingyan XuJia Gu
- 2017
Computer Science
BMC Bioinformatics
Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations.
- 258
- PDF
- Marcel Martin
- 2011
Computer Science, Biology
The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
- 22,238
- PDF
- Ben LangmeadS. Salzberg
- 2012
Computer Science, Biology
Nature Methods
Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
- 39,888
- PDF
- Colby ChiangRyan M. Layer Ira M. Hall
- 2015
Computer Science, Biology
Nature Methods
The SpeedSeq platform accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.
- 452
- PDF
- Heng LiR. Handsaker R. Durbin
- 2009
Computer Science, Biology
Bioinform.
Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by…
- 46,865 [PDF]
- Tom S. SmithA. HegerI. Sudbery
- 2016
Computer Science, Biology
bioRxiv
It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.
- 1,219
- PDF
- Scott R. KennedyMichael W. Schmitt L. Loeb
- 2014
Biology
Nature Protocols
A detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow are provided.
- 360
- PDF
- F. CollynL. GuyM. MarceauM. SimonetClaude-Alain H. Roten
- 2004
Biology
The authors' tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome, and a software package GenomeHalving is created based on this new algorithm, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.
- 28,326
...
...
Related Papers
Showing 1 through 3 of 0 Related Papers