ArticleBMC genomics2018
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 77 citations in OpenAlex.
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- Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae).G3 (Bethesda, Md.) · 2023Article
- Chromosome-Scale Genome Assembly of the Freshwater Snail Semisulcospira habei from the Lake Biwa Drainage System.Genome biology and evolution · 2023Article
- Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior.G3 (Bethesda, Md.) · 2023Article
- Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies.Nature communications · 2023Article
- Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.Genome research · 2023Article
- Hybridisation has shaped a recent radiation of grass-feeding aphids.BMC biology · 2023Article
- The genome of the reef-building glass spongeRoyal Society open science · 2023Article
- Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China.BMC genomic data · 2023Article
- Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis.G3 (Bethesda, Md.) · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundObtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions.
resultsWe present P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs. Tested in various species, P_RNA_scaffolder exhibited higher speed and efficiency than the existing state-of-the-art scaffolders. This tool also improved the contiguity of genome assemblies generated by current mate-pair scaffolding and third-generation single-molecule sequencing assembly.
conclusionsThe P_RNA_scaffolder can improve the contiguity of genome assembly and benefit gene prediction. This tool is available at http://www.fishbrowser.org/software/P_RNA_scaffolder .
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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.