Transcriptome assembly from long-read RNA-seq alignments with StringTie2
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 asse...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-12-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-019-1910-1 |
| _version_ | 1818920926831443968 |
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| author | Sam Kovaka Aleksey V. Zimin Geo M. Pertea Roham Razaghi Steven L. Salzberg Mihaela Pertea |
| author_facet | Sam Kovaka Aleksey V. Zimin Geo M. Pertea Roham Razaghi Steven L. Salzberg Mihaela Pertea |
| author_sort | Sam Kovaka |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T01:29:31Z |
| format | Article |
| id | doaj.art-a59b453d2b4541c696e1a12aa19c7e0d |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-20T01:29:31Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-a59b453d2b4541c696e1a12aa19c7e0d2022-12-21T19:58:08ZengBMCGenome Biology1474-760X2019-12-0120111310.1186/s13059-019-1910-1Transcriptome assembly from long-read RNA-seq alignments with StringTie2Sam Kovaka0Aleksey V. Zimin1Geo M. Pertea2Roham Razaghi3Steven L. Salzberg4Mihaela Pertea5Department of Computer Science, Johns Hopkins UniversityCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins UniversityCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins UniversityCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins UniversityDepartment of Computer Science, Johns Hopkins UniversityCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins UniversityAbstract 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.https://doi.org/10.1186/s13059-019-1910-1Transcriptome assemblyRNA-seqLong-read sequencingGene expression |
| spellingShingle | Sam Kovaka Aleksey V. Zimin Geo M. Pertea Roham Razaghi Steven L. Salzberg Mihaela Pertea Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biology Transcriptome assembly RNA-seq Long-read sequencing Gene expression |
| title | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
| title_full | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
| title_fullStr | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
| title_full_unstemmed | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
| title_short | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
| title_sort | transcriptome assembly from long read rna seq alignments with stringtie2 |
| topic | Transcriptome assembly RNA-seq Long-read sequencing Gene expression |
| url | https://doi.org/10.1186/s13059-019-1910-1 |
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