ArticlePloS one2014
The impacts of read length and transcriptome complexity for de novo assembly: a simulation study.
Article in PloS one, 2014. 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.
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.Bioinformatics and biology insights · 2024Article
- Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data.Non-coding RNA · 2022Article
- Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data.Nature biotechnology · 2022Article
- Transcriptomic profile of the predatory mite Amblyseius swirskii (Acari: Phytoseiidae) on different host plants.Experimental & applied acarology · 2022Article
- Developmental Regulation of Transcription in Touriga Nacional Berries under Deficit Irrigation.Plants (Basel, Switzerland) · 2022Article
- Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
- Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family.Scientific reports · 2021Article
- Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus.Nature communications · 2019Article
- RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat.Scientific reports · 2019Article
- Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.GigaScience · 2019Article
- Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development.G3 (Bethesda, Md.) · 2019Article
- A high-throughput SNP discovery strategy for RNA-seq data.BMC genomics · 2019Article
- A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes.BMC evolutionary biology · 2018Article
- Review
- Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.Viruses · 2017Article
- Article
- Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.International journal of molecular sciences · 2016Article
- An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.BMC bioinformatics · 2015Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve transcriptome assembly, but it is unknown whether the read length really matters. In addition, though many assembly tools are available now, it is unclear whether the existing assemblers perform well enough for all data with different transcriptome complexities. In this paper, we studied these two open problems using two high-performing assemblers, Velvet/Oases and Trinity, on several simulated datasets of human, mouse and S.cerevisiae. The results suggest that (1) the read length of paired reads does not matter once it exceeds a certain threshold, and interestingly, the threshold is distinct in different organisms; (2) the quality of de novo assembly decreases sharply with the increase of transcriptome complexity, all existing de novo assemblers tend to corrupt whenever the genes contain a large number of alternative splicing events.
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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.