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

[1] Accurate isoform discovery with IsoQuant using long reads
Andrey D. Prjibelski
Alla Mikheenko
Anoushka Joglekar
Alexander Smetanin
Julien Jarroux
Alla L. Lapidus
Hagen U. Tilgner
Nature Biotechnology, 2023, 41 : 915 - 918
[2] The Discovery of the Isoquant
Lloyd, Peter
HISTORY OF POLITICAL ECONOMY, 2012, 44 (04) : 643 - 661
[3] Analyzing rare mutations in metagenomes assembled using long and accurate reads
Fedarko, Marcus W.
Kolmogorov, Mikhail
Pevzner, Pavel A.
GENOME RESEARCH, 2022, 32 (11-12) : 2119 - 2133
[4] SAP-A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery
Sun, Zheng
Tian, Weidong
PLOS ONE, 2012, 7 (08):
[5] Assembly-free discovery of human novel sequences using long reads
Li, Qiuhui
Yan, Bin
Lam, Tak-Wah
Luo, Ruibang
DNA RESEARCH, 2022, 29 (06)
[6] Accurate spliced alignment of long RNA sequencing reads
Sahlin, Kristoffer
Makinen, Veli
BIOINFORMATICS, 2021, 37 (24) : 4643 - 4651
[7] Fast and Accurate Algorithms for Mapping and Aligning Long Reads
Yang, Wen
Wang, Lusheng
JOURNAL OF COMPUTATIONAL BIOLOGY, 2021, 28 (08) : 789 - 803
[8] Long Reads Enable Accurate Estimates of Complexity of Metagenomes
Bankevich, Anton
Pevzner, Pavel
RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2018, 2018, 10812 : 1 - 20
[9] Hap10: reconstructing accurate and long polyploid haplotypes using linked reads
Sina Majidian
Mohammad Hossein Kahaei
Dick de Ridder
BMC Bioinformatics, 21
[10] SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads
Luca Denti
Parsoa Khorsand
Paola Bonizzoni
Fereydoun Hormozdiari
Rayan Chikhi
Nature Methods, 2023, 20 : 550 - 558

← 1 2 3 4 5 →