L_RNA_scaffolder: scaffolding genomes with transcripts

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Updating benchtop sequencing performance comparison

(2013) Sebastian Jünemann et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

(2012) T. Takeuchi et al.   DNA RESEARCH

Paired-end sequencing of Fosmid libraries by Illumina

(2012) L. J. S. Williams et al.   GENOME RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach

(2012) Ze Peng et al.   PLoS One

Paired-End Sequencing of Long-Range DNA Fragments for De Novo Assembly of Large, Complex Mammalian Genomes by Direct Intra-Molecule Ligation

(2012) Asan et al.   PLoS One

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

Fast scaffolding with small independent mixed integer programs

(2011) L. Salmela et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

(2011) Song Gao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

ABySS: A parallel assembler for short read sequence data

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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE