ArticleGenome biology2024
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed, 5 citations in OpenAlex.
- A systematic PCR-based framework for amplification of long and multi-exonic genes in non-model insects: : A case study of Bemisia tabaci Asia II 1.Molecular biology reports · 2026Article
- Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).The Journal of heredity · 2025Article
- 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
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off-target RNA contamination. In this manuscript, we present GTax, a taxonomy-structured database of genomic sequences that can be used with BLAST to detect and remove foreign contamination in RNA sequencing samples before assembly. In addition, we use a de novo transcriptome assembly of Solanum lycopersicum (tomato) to demonstrate that removing foreign contamination in sequencing samples reduces the number of assembled chimeric transcripts.
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Registered trials
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