ArticleGenome biology2019
Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.
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 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Minimum flow decomposition guided by saturating subflows.bioRxiv : the preprint server for biology · 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
- Improved reconstruction of transcripts and coding sequences from RNA-seq data.Nucleic acids research · 2026Article
- Review
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- De novo clustering of large long-read transcriptome datasets with isONclust3.Bioinformatics (Oxford, England) · 2025Article
- Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback).Scientific data · 2024Article
- Accurate isoform discovery with IsoQuant using long reads.Nature biotechnology · 2023Article
- isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.Bioinformatics (Oxford, England) · 2023Article
- Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.Genome research · 2022Article
- Accurate assembly of multi-end RNA-seq data with Scallop2.Nature computational science · 2022Article
- Jumper enables discontinuous transcript assembly in coronaviruses.Nature communications · 2021Article
- Review
- Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses inInternational journal of molecular sciences · 2020Article
- Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.Genome biology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing length limits. This drives a need for long-read transcript assembly. By adding long-read-specific optimizations to Scallop, we developed Scallop-LR, a reference-based long-read transcript assembler. Analyzing 26 PacBio samples, we quantified the benefit of performing transcript assembly on long reads. We demonstrate Scallop-LR identifies more known transcripts and potentially novel isoforms for the human transcriptome than Iso-Seq Analysis and StringTie, indicating that long-read transcript assembly by Scallop-LR can reveal a more complete human transcriptome.
Indexed as
Identifiers
What OpenQuestion holds
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.