Transcriptome assembly from long-read RNA-seq alignments with StringTie2
By S. Kovaka, Aleksey V. Zimin, Geo Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea. Genome Biology, 2019
1,681 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9e4310a109f0f2c672d75bdbc51328510a7e6d94
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In Molecular Biology
- Alaina Shumate
- Brandon Wong
- Mihaela Pertea
- Geo Pertea
- Yunhao Wang
- Yue Zhao
- Yuru Wang
- Audrey E. Bollas
Citations in the corpus
- Improved transcriptome assembly using a hybrid of long and short reads with StringTie (2021, methodology): “We used the same short read simulated data from FluxSim [17] as was used to evaluate StringTie2 [9] We used NanoSim [18] to simulate ONT direct RNA sequencing reads.”
- GFF Utilities: GffRead and GffCompare (2020, background): “…both GffRead and GffCompare have already been used in many bioinformatics projects as integral parts of pipelines for genome annotation 5–7 , novel gene discoveries and characterizations 8–18 , gene structure reconstruction accuracy 19–21 , and gene annotation comparisons 22–25 among others.”
- Nanopore sequencing technology, bioinformatics and applications (2021, background): “125 ) and TALON 126 as well as several based on hybrid sequencing data (for example, IDP 127 ).”
- BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, neutral): “Notably, a new type of external hints is created from assembled StringTie2 transcripts [Kovakaet al., 2019].”
- Ensembl 2022 (2021, methodology): “In creating an efficient annotation system, we have incorporated additional software to maximise the value of transcriptomic data including STAR (5) for short read alignments, as well as Scallop (6) and Stringtie2 (7) for transcript reconstruction.”