De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

rnaQUAST: a quality assessment tool forde novotranscriptome assemblies: Table 1.

(2016) Elena Bushmanova et al.   BIOINFORMATICS

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

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

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

(2016) Juntao Liu et al.   PLoS Computational Biology

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus

(2016) Satshil B. Rana et al.   PLoS One

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

(2016) Martin Hölzer et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Transcriptional Stress Response of Candida albicans to Weak Organic Acids

(2015) Fabien Cottier et al.   G3-Genes Genomes Genetics

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

(2015) Zheng Chang et al.   GENOME BIOLOGY

Comparisons of De Novo Transcriptome Assemblers in Diploid and Polyploid Species Using Peanut (Arachis spp.) RNA-Seq Data

(2015) Ratan Chopra et al.   PLoS One

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

MED18 interaction with distinct transcription factors regulates multiple plant functions

(2014) Zhibing Lai et al.   Nature Communications

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome

(2014) Joanna Moreton et al.   Frontiers in Genetics

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

(2013) Yu Peng et al.   BIOINFORMATICS

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq

(2013) BingXin Lu et al.   Science China-Life Sciences

Comparative analysis of de novo transcriptome assembly

(2013) Kaitlin Clarke et al.   Science China-Life Sciences

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

De novo transcriptome assembly of RNA-Seq reads with different strategies

(2012) Geng Chen et al.   Science China-Life Sciences

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

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

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

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS