SPATA: A seeding and patching algorithm for de novo transcriptome assembly

Zhiyu Zhao; Tin Chi Nguyen; Nan Deng; Kristen Marie Johnson; Dongxiao Zhu

doi:10.1109/BIBMW.2011.6112351

SPATA: A seeding and patching algorithm for de novo transcriptome assembly

Zhiyu Zhao, Tin Chi Nguyen, Nan Deng, Kristen Marie Johnson, Dongxiao Zhu

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Scopus citations

Abstract

RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.

Original language	English (US)
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	26-33
Number of pages	8
DOIs	https://doi.org/10.1109/BIBMW.2011.6112351
Publication status	Published - 2011
Event	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States Duration: Nov 12 2011 → Nov 15 2011

Other

Other	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Country	United States
City	Atlanta, GA
Period	11/12/11 → 11/15/11

Fingerprint

Keywords

de novo assembly
read mapping
RNA-seq
transcriptome

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

Cite this

Zhao, Z., Nguyen, T. C., Deng, N., Johnson, K. M., & Zhu, D. (2011). SPATA: A seeding and patching algorithm for de novo transcriptome assembly. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 26-33). [6112351] https://doi.org/10.1109/BIBMW.2011.6112351

Zhao, Z, Nguyen, TC, Deng, N, Johnson, KM & Zhu, D 2011, SPATA: A seeding and patching algorithm for de novo transcriptome assembly. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112351, pp. 26-33, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112351

@inproceedings{f6710649f2d74245855ca1a52db057c5,

title = "SPATA: A seeding and patching algorithm for de novo transcriptome assembly",

abstract = "RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.",

keywords = "de novo assembly, read mapping, RNA-seq, transcriptome",

author = "Zhiyu Zhao and Nguyen, {Tin Chi} and Nan Deng and Johnson, {Kristen Marie} and Dongxiao Zhu",

year = "2011",

doi = "10.1109/BIBMW.2011.6112351",

language = "English (US)",

isbn = "9781457716133",

pages = "26--33",

booktitle = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

note = "2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 ; Conference date: 12-11-2011 Through 15-11-2011",

}

TY - GEN

T1 - SPATA

T2 - 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011

AU - Zhao, Zhiyu

AU - Nguyen, Tin Chi

AU - Deng, Nan

AU - Johnson, Kristen Marie

AU - Zhu, Dongxiao

PY - 2011

Y1 - 2011

N2 - RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.

AB - RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.

KW - de novo assembly

KW - read mapping

KW - RNA-seq

KW - transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84855992328&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84855992328&partnerID=8YFLogxK

U2 - 10.1109/BIBMW.2011.6112351

DO - 10.1109/BIBMW.2011.6112351

M3 - Conference contribution

AN - SCOPUS:84855992328

SN - 9781457716133

SP - 26

EP - 33

BT - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Y2 - 12 November 2011 through 15 November 2011

ER -

Access to Document

10.1109/BIBMW.2011.6112351