Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A comparative study of RNA-seq analysis strategies

(2015) J. Janes et al.   BRIEFINGS IN BIOINFORMATICS

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

(2015) Zheng Chang et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis

(2014) Karlheinz Mann et al.   BMC GENOMICS

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

A Comprehensive Reference Transcriptome Resource for the Common House Spider Parasteatoda tepidariorum

(2014) Nico Posnien et al.   PLoS One

A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly and Utility for RNA-Seq in a Non-Model Bird

(2014) Findley R. Finseth et al.   PLoS One

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

(2013) Yu Peng et al.   BIOINFORMATICS

Assessing De Novo transcriptome assembly metrics for consistency and utility

(2013) Shawn T O’Neil et al.   BMC GENOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome

(2013) Rajesh Ghangal et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

(2012) Jialei Duan et al.   BMC GENOMICS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

(2010) Shawn T O'Neil et al.   BMC GENOMICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

(2008) V. P. Belancio et al.   GENOME RESEARCH