ArticleGenomics data2015
Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler.
Article in Genomics data, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Genomic and metabolomic insights into the biosynthesis of carotenoids and lipids in oleaginous red yeast Cystofilobasidium infirmominiatum HZR20 isolated from Mangrove plants in Southern China.Archives of microbiology · 2025Article
- De Novo transcriptome assembly of Diaprepes abbreviatus: foundations for functional genomics and targeted pest management.BMC genomics · 2025Article
- VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data.Briefings in bioinformatics · 2023Article
- A review of the endangered mollusks transcriptome under the threatened species initiative of Korea.Genes & genomics · 2023Review
- Independent Recruitment of Different Types of Phospholipases A2 to the Venoms of Caenophidian Snakes: The Rise of PLA2-IIE within Pseudoboini (Dipsadidae).Molecular biology and evolution · 2023Article
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- Discovery and genome-guided mapping ofHorticulture research · 2023Article
- RNA-Sequencing of Heterorhabditis nematodes to identify factors involved in symbiosis with Photorhabdus bacteria.BMC genomics · 2022Article
- Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella.BMC ecology and evolution · 2022Article
- Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes.Molecular biology and evolution · 2020Article
- Size Matters: An Evaluation of the Molecular Basis of Ontogenetic Modifications in the Composition ofToxins · 2020Article
- De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress.Scientific reports · 2020Article
- Article
- Comparative transcriptome analyses provide novel insights into the differential response of Pigeonpea (Cajanus cajan L.) and its wild relative (Cajanus platycarpus (Benth.) Maesen) to herbivory by Helicoverpa armigera (Hübner).Plant molecular biology · 2019Article
- Comparative transcriptome analysis of pigeonpea, Cajanus cajan (L.) and one of its wild relatives Cajanus platycarpus (Benth.) Maesen.PloS one · 2019Article
- A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita.BMC genomics · 2018Article
- Article
- A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.BMC genomics · 2017Article
- De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.
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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.