ArticleFrontiers in plant science2012
RNA-Seq Assembly - Are We There Yet?
Article in Frontiers in plant science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation.International journal of molecular sciences · 2024Review
- Variability of plant transcriptomic responses under stress acclimation: a review from high throughput studies.Acta biochimica Polonica · 2024Review
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- Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics.BMC plant biology · 2022Article
- Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.Systematic biology · 2021Article
- Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs ofInternational journal of molecular sciences · 2020Article
- De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.Scientific reports · 2019Article
- De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development.BMC genomics · 2019Article
- De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms.Scientific reports · 2019Article
- Article
- Plant genome and transcriptome annotations: from misconceptions to simple solutions.Briefings in bioinformatics · 2018Article
- A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Frontiers in microbiology · 2018Article
- Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound inFrontiers in plant science · 2018Article
- Article
- K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity.BMC bioinformatics · 2017Article
- RNA-seq of Rice Yellow Stem BorerG3 (Bethesda, Md.) · 2017Article
- Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis.Scientific reports · 2017Article
- De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes.International journal of molecular sciences · 2017Article
- De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages.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
Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species. While some of the databases were successfully used for downstream applications, such as proteomics, the assembly parameters indicate that the assemblies do not yet accurately reflect the actual plant transcriptomes. Two different assembly strategies have been used, overlap consensus based assemblers for long reads and Eulerian path/de Bruijn graph assembler for short reads. In this review, we discuss the challenges and solutions to the transcriptome assembly problem. A list of quality control parameters and the necessary scripts to produce them are provided.
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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.