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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

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

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Parallel short sequence assembly of transcriptomes

(2009) Benjamin G Jackson et al.   BMC BIOINFORMATICS

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

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

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

(2009) Graham A. Heap et al.   HUMAN MOLECULAR GENETICS

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

(2009) M. Yassour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

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

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009

(2008) H. Wakaguri et al.   NUCLEIC ACIDS RESEARCH

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY