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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Vydáno v:	Genome Biology Ročník 20; číslo 1; s. 278
Hlavní autoři:	Kovaka, Sam, Zimin, Aleksey V., Pertea, Geo M., Razaghi, Roham, Salzberg, Steven L., Pertea, Mihaela
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 16.12.2019 Springer Nature B.V BMC
Témata:	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
On-line přístup:	Získat plný text
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Popis
Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-019-1910-1