ArticleNature computational science2022
Accurate assembly of multi-end RNA-seq data with Scallop2.
Article in Nature computational science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Minimum flow decomposition guided by saturating subflows.bioRxiv : the preprint server for biology · 2026Article
- Amaranth: enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads.Bioinformatics (Oxford, England) · 2026Article
- StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts.Nature methods · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads.bioRxiv : the preprint server for biology · 2025Article
- A complete telomere-to-telomere assembly of Oryza sativa L. subsp. indica Kato T197 genome.Scientific data · 2025Article
- Boosting Transcript Assembly via Delineating Transcript Start and End Sites.bioRxiv : the preprint server for biology · 2025Article
- Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy.Communications biology · 2025Article
- Anchorage accurately assembles anchor-flanked synthetic long reads.Algorithms for molecular biology : AMB · 2025Article
- Transcriptome assembly at single-cell resolution with Beaver.Bioinformatics (Oxford, England) · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Building better genome annotations across the tree of life.Genome research · 2025Article
- Accurate assembly of multiple RNA-seq samples with Aletsch.Bioinformatics (Oxford, England) · 2024Article
- Chromosome-level genome assembly of the silver pomfret Pampus argenteus.Scientific data · 2024Article
- Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2024Article
- Transcript assembly and annotations: Bias and adjustment.PLoS computational biology · 2023Article
- OnACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Modern RNA-sequencing protocols can produce multi-end data, where multiple reads originating from the same transcript are attached to the same barcode. The long-range information in the multi-end reads is beneficial in phasing complicated spliced isoforms, but assembly algorithms that leverage such information are lacking. Here we introduce Scallop2, a reference-based assembler optimized for multi-end RNA-seq data. The algorithmic core of Scallop2 consists of three steps: (1) using an algorithm to "bridge" multi-end reads into single-end phasing paths in the context of a splice graph, (2) employing a method to refine erroneous splice graphs by utilizing multi-end reads that fail to bridge, and (3) piping the refined splice graph and the bridged phasing paths into an algorithm that integrates multiple phase-preserving decompositions. Tested on 561 cells in two Smart-seq3 datasets and on 10 Illumina paired-end RNA-seq samples, Scallop2 substantially improves the assembly accuracy compared to two popular assemblers StringTie2 and Scallop.
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Registered trials
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.