Abstract

Abstract 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.

Keywords

TranscriptomeBiologyComputational biologyRNA-SeqSequence assemblyRNAk-merDeep sequencingGeneticsDNA sequencingComputer scienceBioinformaticsGenomeGeneGene expression

MeSH Terms

AnimalsArabidopsisGenetic TechniquesGenomicsHumansSequence AnalysisRNASoftwareTranscriptomeZea mays

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Publication Info

Year
2019
Type
article
Volume
20
Issue
1
Pages
278-278
Citations
1857
Access
Closed

External Links

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Cite This

Sam Kovaka, Aleksey V. Zimin, Geo Pertea et al. (2019). Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome biology , 20 (1) , 278-278. https://doi.org/10.1186/s13059-019-1910-1

Identifiers

DOI
10.1186/s13059-019-1910-1
PMID
31842956
PMCID
PMC6912988

Data Quality

Data completeness: 90%