Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

FRAMA: from RNA-seq data to annotated mRNA assemblies

(2016) Martin Bens et al.   BMC GENOMICS

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

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

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

(2016) Loren A. Honaas et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms

(2015) Stanley Kimbung Mbandi et al.   BMC BIOINFORMATICS

Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms

(2015) Bin He 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

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

(2013) Ya Yang et al.   BMC GENOMICS

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

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

(2012) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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