ArticleGenome biology2019
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Review
- SpliSync: Genomic language model-driven splice site correction of long RNA sequencing reads.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Identification of cell-type-specific, transcriptionally active transposable elements using long-read RNA-sequencing data-based comprehensive annotation.Genomics & informatics · 2025Article
- Article
- Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling.Cell genomics · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- xRead: a coverage-guided approach for scalable construction of read overlapping graph.GigaScience · 2025Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- GIN-TONIC: non-hierarchical full-text indexing for graph genomes.NAR genomics and bioinformatics · 2024Article
- Profiles of phenolics and their synthetic pathways inFood chemistry. Molecular sciences · 2024Article
- Characterization of alternative splicing during mammalian brain development reveals the extent of isoform diversity and potential effects on protein structural changes.Biology open · 2024Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Accurate isoform discovery with IsoQuant using long reads.Nature biotechnology · 2023Article
- isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.Bioinformatics (Oxford, England) · 2023Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.bioRxiv : the preprint server for biology · 2023Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
- Steroidal saponin profiles and their key genes for synthesis and regulation in Asparagus officinalis L. by joint analysis of metabolomics and transcriptomics.BMC plant biology · 2023Article
- ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data.Science advances · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The alignment of long-read RNA sequencing reads is non-trivial due to high sequencing errors and complicated gene structures. We propose deSALT, a tailored two-pass alignment approach, which constructs graph-based alignment skeletons to infer exons and uses them to generate spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and sequencing errors, which break through bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that deSALT has a greater ability to produce accurate and homogeneous full-length alignments. deSALT is available at: https://github.com/hitbc/deSALT.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.