Accurate isoform discovery with IsoQuant using long reads

被引：49

作者：

Prjibelski, Andrey D. ^{[1
,2
]}

Mikheenko, Alla ^{[1
]}

Joglekar, Anoushka ^{[3
,4
,5
]}

Smetanin, Alexander ^{[6
]}

Jarroux, Julien ^{[4
,5
]}

Lapidus, Alla L. ^{[1
]}

Tilgner, Hagen U. ^{[4
,5
]}

机构：

[1] St Petersburg State Univ, Inst Translat Biomed, Ctr Algorithm Biotechnol, St Petersburg, Russia

[2] Univ Helsinki, Dept Comp Sci, Helsinki, Finland

[3] Weill Cornell Med, Triinst Computat Biol & Med, New York, NY USA

[4] Weill Cornell Med, Brain & Mind Res Inst, New York, NY 10021 USA

[5] Weill Cornell Med, Ctr Neurogenet, New York, NY 10021 USA

[6] Bioinformat Inst, St Petersburg, Russia

来源：

NATURE BIOTECHNOLOGY | 2023年 / 41卷 / 07期

关键词：

Computational tools - False positive rates - Free mode - Genome annotation - Improve performance - Isoforms - Reference-free;

D O I：

10.1038/s41587-022-01565-y

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data.

引用

页码：915 / +

页数：10

共 50 条

[21] Full-Length rAAV Sequencing for Mixture Population Characterization Using Highly Accurate Long Reads
Tseng, Elizabeth
Dhillon, Harsharan
Volden, Roger
MOLECULAR THERAPY, 2023, 31 (04) : 776 - 776
[22] Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
Ma, Jun
Caceres, Manuel
Salmela, Leena
Makinen, Veli
Tomescu, Alexandru, I
BIOINFORMATICS, 2023, 39 (08)
[23] Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
Hotaling, Scott
Wilcox, Edward R.
Heckenhauer, Jacqueline
Stewart, Russell J.
Frandsen, Paul B.
BMC GENOMICS, 2023, 24 (01)
[24] Ultra-accurate microbial amplicon sequencing with synthetic long reads
Callahan, Benjamin J.
Grinevich, Dmitry
Thakur, Siddhartha
Balamotis, Michael A.
Ben Yehezkel, Tuval
MICROBIOME, 2021, 9 (01)
[25] Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
Scott Hotaling
Edward R. Wilcox
Jacqueline Heckenhauer
Russell J. Stewart
Paul B. Frandsen
BMC Genomics, 24
[26] Ultra-accurate microbial amplicon sequencing with synthetic long reads
Benjamin J. Callahan
Dmitry Grinevich
Siddhartha Thakur
Michael A. Balamotis
Tuval Ben Yehezkel
Microbiome, 9
[27] Comprehensive variant detection in a human genome with highly accurate long reads
Rowell, W. J.
Wenger, A. M.
Kolesnikov, A.
Chang, P.
Carroll, A.
Hall, R. J.
Peluso, P.
EUROPEAN JOURNAL OF HUMAN GENETICS, 2019, 27 : 1723 - 1723
[28] Fast and Accurate Classification of Meta-Genomics Long Reads With deSAMBA
Li, Gaoyang
Liu, Yongzhuang
Li, Deying
Liu, Bo
Li, Junyi
Hu, Yang
Wang, Yadong
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2021, 9
[29] ARAMIS: From systematic errors of NGS long reads to accurate assemblies
Sacristan-Horcajada, E.
Gonzalez-de la Fuente, S.
Peiro-Pastor, R.
Carrasco-Ramiro, F.
Amils, R.
Requena, J. M.
Berenguer, J.
Aguado, B.
BRIEFINGS IN BIOINFORMATICS, 2021, 22 (06)
[30] Full-length isoform sequencing of the human MCF-7 cell line using PacBio long reads
Tseng, Elizabeth
Clark, Tyson
Ashby, Meredith H.
Shenykman, Gloria
CANCER RESEARCH, 2015, 75

← 1 2 3 4 5 →