ArticleGigaScience2015
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 296 papers.
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296 citing papers in PubMed.
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- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
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- Deciphering the biosynthetic pathways of lichen acids.The New phytologist · 2026Article
- Chromosome-Level Reference Genome of the Beach False Foxglove, Agalinis fasciculata (Orobanchaceae).Genome biology and evolution · 2026Article
- Integrated transcriptomic and proteomic analysis of cancer-suppressive Mesocestoides corti larvae.Parasites & vectors · 2026Article
- Exploring the visual system of the black grouse (Lyrurus tetrix): combining experimental and molecular approaches to inform strategies for reducing collisions.The Journal of experimental biology · 2026Article
- Transcriptomic dataset of two types of coelomocytes fromData in brief · 2026Article
- Expansion of the geranylgeranyl pyrophosphate synthase gene family underlies the evolution of terpenoid biosynthesis in termites.PLoS biology · 2026Article
- Genetic parallelism underpins convergent mimicry coloration in Lepidoptera across 120 million years of evolution.PLoS biology · 2026Article
236 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.
findingsWe developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read.
conclusionsRcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.
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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.