AGOUTI: improving genome assembly and annotation using transcriptome data

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome

(2015) Meili Chen et al.   Scientific Reports

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Visualization and quality assessment of de novo genome assemblies

(2011) Oksana Riba-Grognuz et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Scaffolding a Caenorhabditis nematode genome with RNA-seq

(2010) A. Mortazavi et al.   GENOME RESEARCH

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE