Informedkmer selection forde novotranscriptome assembly

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

(2015) Zheng Chang et al.   GENOME BIOLOGY

Fiona: a parallel and automatic strategy for read error correction

(2014) Marcel H. Schulz et al.   BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

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

(2014) Y. Xie et al.   BIOINFORMATICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

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

(2013) Yu Peng et al.   BIOINFORMATICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Probabilistic error correction for RNA sequencing

(2013) Hai-Son Le et al.   NUCLEIC ACIDS RESEARCH

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

(2012) Berat Z Haznedaroglu et al.   BMC BIOINFORMATICS

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

(2011) DANIEL B. SLOAN et al.   Molecular Ecology Resources

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

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

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

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

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

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

(2008) M. Sultan et al.   SCIENCE