Transcriptome assembly from long-read RNA-seq alignments with StringTie2

RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler tha...

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Bibliographic Details
Published in:Genome Biology Vol. 20; no. 1; p. 278
Main Authors: Kovaka, Sam, Zimin, Aleksey V., Pertea, Geo M., Razaghi, Roham, Salzberg, Steven L., Pertea, Mihaela
Format: Journal Article
Language:English
Published: London BioMed Central 16.12.2019
Springer Nature B.V
BMC
Subjects:
Accuracy
Animal Genetics and Genomics
Animals
Annotations
Arabidopsis
Bioinformatics
Biomedical and Life Sciences
Evolutionary Biology
Gene expression
Genes
Genetic Techniques
genome
Genomes
Genomics - methods
Human Genetics
Humans
Life Sciences
Long-read sequencing
Method
Microbial Genetics and Genomics
Nucleotides
Plant Genetics and Genomics
Proteins
Ribonucleic acid
RNA
RNA-seq
sequence analysis
Sequence Analysis, RNA
Software
Transcriptome
Transcriptome assembly
Zea mays
Long-read sequencing
Transcriptome assembly
RNA-seq
Gene expression
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Summary:RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies. StringTie2 is more accurate and faster and uses less memory than all comparable short-read and long-read analysis tools.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1910-1