QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

Xiangjun Ji; Weida Tong; Baitang Ning; Christopher E. Mason; David P. Kreil; Pawel P. Labaj; Geng Chen; Tieliu Shi

doi:10.1007/s11427-018-9433-3

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

Xiangjun Ji
, Weida Tong
, Baitang Ning
, Christopher E. Mason
, David P. Kreil
, Pawel P. Labaj
, Geng Chen^*
, Tieliu Shi

^*Corresponding author for this work

School of Life Sciences

East China Normal University
United States Food and Drug Administration
Cornell University
The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine
University of Natural Resources and Life Sciences, Vienna
Jagiellonian University in Kraków
Austrian Academy of Sciences

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

8 Scopus citations

Abstract

RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5% more low abundance (0.1–1 FPKM) transcripts with over 2.1% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/.

Original language	English
Pages (from-to)	937-946
Number of pages	10
Journal	Science China Life Sciences
Volume	62
Issue number	7
DOIs	https://doi.org/10.1007/s11427-018-9433-3
State	Published - 1 Jul 2019

Keywords

RNA-Seq
transcript assembly
transcript quantification
transcriptome reconstruction

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10.1007/s11427-018-9433-3

Cite this

@article{c1ed0160e16e4089be4aba18046bb17b,

title = "QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm",

abstract = "RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5\% more low abundance (0.1–1 FPKM) transcripts with over 2.1\% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/.",

keywords = "RNA-Seq, transcript assembly, transcript quantification, transcriptome reconstruction",

author = "Xiangjun Ji and Weida Tong and Baitang Ning and Mason, \{Christopher E.\} and Kreil, \{David P.\} and Labaj, \{Pawel P.\} and Geng Chen and Tieliu Shi",

note = "Publisher Copyright: {\textcopyright} 2019, Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.",

year = "2019",

month = jul,

day = "1",

doi = "10.1007/s11427-018-9433-3",

language = "英语",

volume = "62",

pages = "937--946",

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T1 - QuaPra

T2 - Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

AU - Ji, Xiangjun

AU - Tong, Weida

AU - Ning, Baitang

AU - Mason, Christopher E.

AU - Kreil, David P.

AU - Labaj, Pawel P.

AU - Chen, Geng

AU - Shi, Tieliu

PY - 2019/7/1

Y1 - 2019/7/1

N2 - RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5% more low abundance (0.1–1 FPKM) transcripts with over 2.1% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/.

AB - RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5% more low abundance (0.1–1 FPKM) transcripts with over 2.1% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/.

KW - RNA-Seq

KW - transcript assembly

KW - transcript quantification

KW - transcriptome reconstruction

UR - https://www.scopus.com/pages/publications/85066890401

U2 - 10.1007/s11427-018-9433-3

DO - 10.1007/s11427-018-9433-3

M3 - 文章

C2 - 31124003

AN - SCOPUS:85066890401

SN - 1674-7305

VL - 62

SP - 937

EP - 946

JO - Science China Life Sciences

JF - Science China Life Sciences

IS - 7

ER -

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

Abstract

Keywords

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