ArticlePLoS computational biology2017
Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Integrative multiomic analysis reveals co-ordinated alternative splicing in human bone marrow stromal stem cells.Scientific reports · 2026Article
- Coordinated molecular and physiological adaptations enable activity at sub-freezing temperatures in the snow fly Chionea alexandriana.Current biology : CB · 2026Article
- Near-complete genome assembly of a transformation-efficient elite inbred line LH244 and its comparison with B73.Journal of integrative plant biology · 2026Article
- Large DNA and protein language models enhance discovery of deleterious mutations in maize.Genome biology · 2025Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- Exploring the Linkage Between Ruminal Microbial Communities on Postweaning and Finishing Diets and Their Relation to Residual Feed Intake in Beef Cattle.Microorganisms · 2024Article
- The genome of Eleocharis vivipara elucidates the genetics of CJournal of integrative plant biology · 2024Article
- Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis.BMC genomics · 2024Article
- High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres.Plant communications · 2024Article
- StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads.Genes & genomics · 2023Article
- A happy accident: a novel turfgrass reference genome.G3 (Bethesda, Md.) · 2023Article
- RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer.Cell reports · 2023Article
- Improving RNA Assembly via Safety and Completeness in Flow Decompositions.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data.Non-coding RNA · 2022Article
- Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.Frontiers in plant science · 2022Review
- De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science (New York, N.Y.) · 2021Article
- SAUTE: sequence assembly using target enrichment.BMC bioinformatics · 2021Article
- FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.BMC bioinformatics · 2021Article
- Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis.BMC genomics · 2021Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. AVAILABILITY: Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.
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