ArticleGenome research2010
Optimization of de novo transcriptome assembly from next-generation sequencing data.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers.
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Who cites it
203 citing papers in PubMed, 344 citations in OpenAlex.
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- Assembled and annotated reference genome and demographic history of the eastern chipmunk (Tamias striatus).Molecular genetics and genomics : MGG · 2026Article
- Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information.Communications biology · 2025Article
- Classification of and detection techniques for RNAi-induced effects in GM plants.Frontiers in plant science · 2025Review
- Roast: a tool for reference-free optimization of supertranscriptome assemblies.BMC bioinformatics · 2024Article
- Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis.Scientific reports · 2023Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Metabolomics and transcriptomics analyses for characterizing the alkaloid metabolism of Chinese jujube and sour jujube fruits.Frontiers in plant science · 2023Article
- Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study inPlants (Basel, Switzerland) · 2022Article
- Transcriptional expression changes during compensatory plasticity in the terminal ganglion of the adult cricket Gryllus bimaculatus.BMC genomics · 2021Article
- Transcriptome Signature of Immune Cells Post Reovirus Treatment inCancer management and research · 2021Article
- Salivary and Intestinal Transcriptomes Reveal Differential Gene Expression in Starving, Fed andFrontiers in cellular and infection microbiology · 2021Article
- Review
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- Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Frontiers in plant science · 2020Article
- Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut.PloS one · 2020Article
- Comparative Analysis of Strategies forHigh-throughput · 2019Article
- BHap: a novel approach for bacterial haplotype reconstruction.Bioinformatics (Oxford, England) · 2019Article
- Utilization of Tissue Ploidy Level Variation inG3 (Bethesda, Md.) · 2019Article
- Biosynthesis and Signal Transduction of ABA, JA, and BRs in Response to Drought Stress of Kentucky Bluegrass.International journal of molecular sciences · 2019Article
143 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome analysis has important applications in many biological fields. However, assembling a transcriptome without a known reference remains a challenging task requiring algorithmic improvements. We present two methods for substantially improving transcriptome de novo assembly. The first method relies on the observation that the use of a single k-mer length by current de novo assemblers is suboptimal to assemble transcriptomes where the sequence coverage of transcripts is highly heterogeneous. We present the Multiple-k method in which various k-mer lengths are used for de novo transcriptome assembly. We demonstrate its good performance by assembling de novo a published next-generation transcriptome sequence data set of Aedes aegypti, using the existing genome to check the accuracy of our method. The second method relies on the use of a reference proteome to improve the de novo assembly. We developed the Scaffolding using Translation Mapping (STM) method that uses mapping against the closest available reference proteome for scaffolding contigs that map onto the same protein. In a controlled experiment using simulated data, we show that the STM method considerably improves the assembly, with few errors. We applied these two methods to assemble the transcriptome of the non-model catfish Loricaria gr. cataphracta. Using the Multiple-k and STM methods, the assembly increases in contiguity and in gene identification, showing that our methods clearly improve quality and can be widely used. The new methods were used to assemble successfully the transcripts of the core set of genes regulating tooth development in vertebrates, while classic de novo assembly failed.
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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.