4.7 Article

Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

Morteza Sheikh-Assadi et al.

Summary: This study investigated the genetic diversity and evolutionary history of Lilium ledebourii by obtaining its whole chloroplast genome and conducting comparative analysis with other species in the Lilium genus. The results revealed the specific structure and diverse gene content of the chloroplast genome of L. ledebourii, with higher variability in certain regions. The phylogenetic analysis of Lilium reconstructed a new tree and identified positive selection in some chloroplast protein-coding genes. These findings are significant for species identification, population genetics, and conservation of Lilium.

SCIENTIFIC REPORTS (2022)

Article Biochemical Research Methods

A consensus-based ensemble approach to improve transcriptome assembly

Adam Voshall et al.

Summary: This study introduces a new ensemble transcriptome assembly method, ConSemble, which improves the accuracy of transcriptome assembly without the need for a reference genome and also enhances the precision of genome-guided assembly with a reference genome.

BMC BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Mohammad Sadat-Hosseini et al.

PLOS ONE (2020)

Article Multidisciplinary Sciences

One thousand plant transcriptomes and the phylogenomics of green plants

James H. Leebens-Mack et al.

NATURE (2019)

Article Biotechnology & Applied Microbiology

TransLiG: a de novo transcriptome assembler that uses line graph iteration

Juntao Liu et al.

GENOME BIOLOGY (2019)

Review Plant Sciences

A guide to sequence your favorite plant genomes

Fay-Wei Li et al.

APPLICATIONS IN PLANT SCIENCES (2018)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies

Elena Bushmanova et al.

BIOINFORMATICS (2016)

Article Evolutionary Biology

De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata

Ann Kathrin Huylmans et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

TransRate: reference-free quality assessment of de novo transcriptome assemblies

Richard Smith-Unna et al.

GENOME RESEARCH (2016)

Article Biochemical Research Methods

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Juntao Liu et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

Erik A. Visser et al.

BMC GENOMICS (2015)

Article Biotechnology & Applied Microbiology

Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms

Bin He et al.

BMC GENOMICS (2015)

Article Biotechnology & Applied Microbiology

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

Zheng Chang et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Evaluation of de novo transcriptome assemblies from RNA-Seq data

Bo Li et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Assessing De Novo transcriptome assembly metrics for consistency and utility

Shawn T. O'Neil et al.

BMC GENOMICS (2013)

Article Biochemical Research Methods

Streaming fragment assignment for real-time analysis of sequencing experiments

Adam Roberts et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

Assessment of transcript reconstruction methods for RNA-seq

Tamara Steijger et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Marcel H. Schulz et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Qiong-Yi Zhao et al.

BMC BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Review Genetics & Heredity

Next-generation transcriptome assembly

Jeffrey A. Martin et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Optimization of de novo transcriptome assembly from next-generation sequencing data

Yann Surget-Groba et al.

GENOME RESEARCH (2010)