ArticleEcology and evolution2019
The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras.
Article in Ecology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Gut metatranscriptomics based de novo assembly reveals microbial signatures predicting immunotherapy outcomes in non-small cell lung cancer.Journal of translational medicine · 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
- A chromosome-level genome assembly for the dugong (Dugong dugon).The Journal of heredity · 2024Article
- Lipases and carboxylesterases affect moth sex pheromone compounds involved in interspecific mate recognition.Nature communications · 2023Article
- Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae).Scientific reports · 2023Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- Sex-basedGigaByte (Hong Kong, China) · 2022Article
- The Arabinogalactan Protein Family ofPlants (Basel, Switzerland) · 2021Article
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.PLoS computational biology · 2021Article
- Chromosome-Scale Genome Assembly and Transcriptome Assembly of KawakawaFrontiers in genetics · 2021Article
- The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras.Ecology and evolution · 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome quality control is an important step in RNA-Seq experiments. However, the quality of de novo assembled transcriptomes is difficult to assess, due to the lack of reference genome to compare the assembly to. We developed a method to assess and improve the quality of de novo assembled transcriptomes by focusing on the removal of chimeric sequences. These chimeric sequences can be the result of faulty assembled contigs, merging two transcripts into one. The developed method is incorporated into a pipeline, which we named Bellerophon, that is broadly applicable and easy to use. Bellerophon first uses the quality assessment tool TransRate to indicate the quality, after which it uses a transcripts per million (TPM) filter to remove lowly expressed contigs and CD-HIT-EST to remove highly identical contigs. To validate the quality of this method, we performed three benchmark experiments: (1) a computational creation of chimeras, (2) identification of chimeric contigs in a transcriptome assembly, (3) a simulated RNA-Seq experiment using a known reference transcriptome. Overall, the Bellerophon pipeline was able to remove between 40% and 91.9% of the chimeras in transcriptome assemblies and removed more chimeric than nonchimeric contigs. Thus, the Bellerophon sequence of filtration steps is a broadly applicable solution to improve transcriptome assemblies.
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.