FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads: Article No. 345

Xiaoshuang Liu; Zhenhe Yan; Chao Wu; Yang Yang; Xiaomin Li; Guangxin Zhang

doi:10.1186/s12859-019-2936-9

FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads: Article No. 345

Xiaoshuang Liu, Zhenhe Yan, Chao Wu, Yang Yang, Xiaomin Li, Guangxin Zhang

Biosciences Center

Research output: Contribution to journal › Article › peer-review

15 Scopus Citations

Abstract

Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is also very flexible and can implement different functions using different user-set parameter combinations.

Original language	American English
Number of pages	6
Journal	BMC Bioinformatics
Volume	20
DOIs	https://doi.org/10.1186/s12859-019-2936-9
State	Published - 2019

NREL Publication Number

NREL/JA-2700-74302

Keywords

adapter removing
NGS
quality control

Access to Document

10.1186/s12859-019-2936-9

https://www.nrel.gov/docs/fy19osti/74302.pdf

Cite this

@article{eb39233738cc41c79d3d62370cbf8bdf,

title = "FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads: Article No. 345",

abstract = "Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is also very flexible and can implement different functions using different user-set parameter combinations.",

keywords = "adapter removing, NGS, quality control",

author = "Xiaoshuang Liu and Zhenhe Yan and Chao Wu and Yang Yang and Xiaomin Li and Guangxin Zhang",

year = "2019",

doi = "10.1186/s12859-019-2936-9",

language = "American English",

volume = "20",

journal = "BMC Bioinformatics",

issn = "1471-2105",

publisher = "BioMed Central Ltd.",

}

TY - JOUR

T1 - FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads

T2 - Article No. 345

AU - Liu, Xiaoshuang

AU - Yan, Zhenhe

AU - Wu, Chao

AU - Yang, Yang

AU - Li, Xiaomin

AU - Zhang, Guangxin

PY - 2019

Y1 - 2019

N2 - Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is also very flexible and can implement different functions using different user-set parameter combinations.

AB - Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is also very flexible and can implement different functions using different user-set parameter combinations.

KW - adapter removing

KW - NGS

KW - quality control

UR - http://www.scopus.com/inward/record.url?scp=85067378782&partnerID=8YFLogxK

U2 - 10.1186/s12859-019-2936-9

DO - 10.1186/s12859-019-2936-9

M3 - Article

SN - 1471-2105

VL - 20

JO - BMC Bioinformatics

JF - BMC Bioinformatics

ER -

FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads: Article No. 345

Abstract

NREL Publication Number

Keywords

Access to Document

Other files and links

Fingerprint

Cite this