Transcriptome assembly from long-read RNA-seq alignments with StringTie2
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Summary
StringTie2 is a reference-guided transcriptome assembler that works with both short and 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.
- Type
- preprint
- Published
- 2019-07-08
- Cited by
- 1,716
- References
- 58
- Access
- Open access
- OpenAlex
- https://openalex.org/W2954482858
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:198273586
Keywords
Memory footprint, Transcriptome, Computer science, Computational biology, RNA-Seq
References
- PBSIM: PacBio reads simulator - toward accurate genome assembly
- QuorUM: An Error Corrector for Illumina Reads
- Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data
- Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- Improved data analysis for the MinION nanopore sequencer
- Bayesian transcriptome assembly
- Integrative Genomics Viewer
- The advantages of SMRT sequencing
- Transcriptome and genome sequencing uncovers functional variation in humans
- Modelling and simulating generic RNA-Seq experiments with the flux simulator
- Characterization of the human ESC transcriptome by hybrid sequencing
- Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
- L_RNA_scaffolder: scaffolding genomes with transcripts
- HISAT: a fast spliced aligner with low memory requirements
- StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
- GMAP: a genomic mapping and alignment program for mRNA and EST sequence
- Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
- Spontaneous mapping of number and space in adults and young children
- The MaSuRCA genome assembler
Cited by
- The full-length transcriptome of C. elegans using direct RNA sequencing
- Alignment and mapping methodology influence transcript abundance estimation
- Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas
- Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2
- RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
- A conserved role for SFPQ in repression of pathogenic cryptic last exons
- Computational Oncology in the Multi-Omics Era: State of the Art
- Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae.
- GFF Utilities: GffRead and GffCompare
- Genomic diversity of 39 samples of Pyropia species grown in Japan
- Research Techniques Made Simple: Whole-Transcriptome Sequencing by RNA-Seq for Diagnosis of Monogenic Disorders
- Oxford Nanopore sequencing: new opportunities for plant genomics?
- A consensus-based ensemble approach to improve transcriptome assembly
- Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons
- Quantification of translation uncovers the functions of the alternative transcriptome
- A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference
- Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation
- The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp
- Illuminating the dark side of the human transcriptome with long read transcript sequencing
- Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
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