The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

A graph-based approach to diploid genome assembly

(2018) Shilpa Garg et al.   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

Draft genome assembly of the invasive cane toad, Rhinella marina

(2018) Richard J Edwards et al.   GigaScience

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

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

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

(2018) Weiwen Wang et al.   BMC GENOMICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Draft genome sequence of an inbred line ofChenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

(2016) Yasuo Yasui et al.   DNA RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Evaluating carbon storage in restoration plantings in the Tasmanian Midlands, a highly modified agricultural landscape

(2015) Lynda D. Prior et al.   RANGELAND JOURNAL

Evidence for local climate adaptation in early-life traits of Tasmanian populations of Eucalyptus pauciflora

(2015) Archana Gauli et al.   Tree Genetics & Genomes

Diurnal and seasonal variation in light and dark respiration in field-grownEucalyptus pauciflora

(2015) Danielle A. Way et al.   TREE PHYSIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Effect of forest fragmentation and altitude on the mating system of Eucalyptus pauciflora (Myrtaceae)

(2014) Archana Gauli et al.   AUSTRALIAN JOURNAL OF BOTANY

Molecular genetic diversity and population structure in Eucalyptus pauciflora subsp. pauciflora (Myrtaceae) on the island of Tasmania

(2014) Archana Gauli et al.   AUSTRALIAN JOURNAL OF BOTANY

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

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

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

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Rapid hydraulic recovery inEucalyptus paucifloraafter drought: linkages between stem hydraulics and leaf gas exchange

(2013) SEBASTIÀ MARTORELL et al.   PLANT CELL AND ENVIRONMENT

CGAL: computing genome assembly likelihoods

(2013) Atif Rahman et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Survey of the genetic information carried in the genome of Eucalyptus camaldulensis

(2011) Hideki Hirakawa et al.   Plant Biotechnology

Species Discrimination, Population Structure and Linkage Disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis Using SSR Markers

(2011) Shanmugapriya Arumugasundaram et al.   PLoS One

Nocturnal water loss in mature subalpineEucalyptus delegatensistall open forests and adjacentE. pauciflorawoodlands

(2011) Thomas N. Buckley et al.   Ecology and Evolution

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae

(2009) Janet P Slovin et al.   Plant Methods

Uptake of inorganic and amino acid nitrogen from soil by Eucalyptus regnans and Eucalyptus pauciflora seedlings

(2009) C. R. Warren   TREE PHYSIOLOGY