ArticleBioinformatics (Oxford, England)2023
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Review
- Article
- Article
- NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis.Bioinformatics (Oxford, England) · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- Telomere-to-Telomere gap-free genome assembly of the allotetraploid wild raspberry Rubus alceifolius Poir.Scientific data · 2026Article
- Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression.bioRxiv : the preprint server for biology · 2026Article
- Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies.bioRxiv : the preprint server for biology · 2026Article
- Unraveling forensic timelines using molecular markers in Phormia regina maggots.PLoS genetics · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Intron retention regulates STAT2 function and predicts immunotherapy response in lung cancer.bioRxiv : the preprint server for biology · 2025Article
- Empowering bioinformatics communities with Nextflow and nf-core.Genome biology · 2025Review
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- High-quality chromosome-level genome assembly of the whitespotted conger (Conger myriaster).Scientific data · 2025Article
- nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Chromosome-level genome sequencing and assembly of the parasitoid wasp Leptopilina myrica.Scientific data · 2025Article
- Near complete genome assembly of Yadong trout (Salmo trutta).Scientific data · 2025Article
- TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.Genes · 2024Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
motivationIso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms. AVAILABILITY AND IMPLEMENTATION: The pipeline is freely available online on the nf-core website (https://nf-co.re/isoseq) and on GitHub (https://github.com/nf-core/isoseq) under MIT License (DOI: 10.5281/zenodo.7116979).
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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.