Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)

An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black and White Abalone Species

(2019) Rick Masonbrink et al.   Genome Biology and Evolution

Genome Sequencing of Blacklip and Greenlip Abalone for Development and Validation of a SNP Based Genotyping Tool

(2019) James Kijas et al.   Frontiers in Genetics

OUP accepted manuscript

(2018)   BIOINFORMATICS

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

(2018) Bai-Han Zhu et al.   BMC GENOMICS

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

(2018) Mun Hua Tan et al.   GigaScience

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)

(2018) Giulio Formenti et al.   GigaScience

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

The unprecedented 2015/16 Tasman Sea marine heatwave

(2017) Eric C. J. Oliver et al.   Nature Communications

De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read

(2017) Christopher M. Austin et al.   GigaScience

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae

(2017) Bo-Hye Nam et al.   GigaScience

Contrasting patterns of population connectivity between regions in a commercially important molluscHaliotis rubra: integrating population genetics, genomics and marine LiDAR data

(2016) A. D. Miller et al.   MOLECULAR ECOLOGY

Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage

(2016) Mahul Chakraborty et al.   NUCLEIC ACIDS RESEARCH

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

(2016) Chengxi Ye et al.   Scientific Reports

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

De Novo Characterisation of the Greenlip Abalone Transcriptome (Haliotis laevigata) with a Focus on the Heat Shock Protein 70 (HSP70) Family

(2014) Brett P. Shiel et al.   MARINE BIOTECHNOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

World Abalone Supply, Markets, and Pricing: 2011 Update

(2013) H. Roy Gordon et al.   JOURNAL OF SHELLFISH RESEARCH

Acclimation-dependent expression of heat shock protein 70 in Pacific abalone (Haliotis discus hannai Ino) and its acute response to thermal exposure

(2012) Jiaqi Li et al.   CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubraLeach) using selective DNA pooling

(2008) M. Baranski et al.   ANIMAL GENETICS