Genomic architecture and introgression shape a butterfly radiation

…, B Clavijo, J Davey, RB Dikow, G García-Accinelli… - Science, 2019 - science.org
We used 20 de novo genome assemblies to probe the speciation history and architecture of
gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete …

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

D Mapleson, G Garcia Accinelli, G Kettleborough… - …, 2017 - academic.oup.com
Motivation De novo assembly of whole genome shotgun (WGS) next-generation sequencing
(NGS) data benefits from high-quality input with high coverage. However, in practice, …

[HTML][HTML] The ash dieback invasion of Europe was founded by two genetically divergent individuals

…, DGO Saunders, G Garcia Accinelli… - Nature Ecology & …, 2018 - nature.com
Accelerating international trade and climate change make pathogen spread an increasing
concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen …

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

BJ Clavijo, G Garcia Accinelli, J Wright, D Heavens… - BioRxiv, 2017 - biorxiv.org
Producing high-quality whole-genome shotgun de novo assemblies from plant and animal
species with large and complex genomes using low-cost short read sequencing technologies …

[HTML][HTML] Multiple wheat genomes reveal global variation in modern breeding

…, C Gutwin, A Fiebig, C Fosker, BX Fu, GG Accinelli… - Nature, 2020 - nature.com
Advances in genomics have expedited the improvement of several agriculturally important
crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely …

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for …

…, C Schudoma, GG Accinelli, G Kaithakottil… - Genome …, 2017 - genome.cshlp.org
Advances in genome sequencing and assembly technologies are generating many high-quality
genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as …

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

WB Jiao, GG Accinelli, B Hartwig, C Kiefer… - Genome …, 2017 - genome.cshlp.org
Long-read sequencing can overcome the weaknesses of short reads in the assembly of
eukaryotic genomes; however, at present additional scaffolding is needed to achieve …

A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost

D Heavens, GG Accinelli, B Clavijo, MD Clark - Biotechniques, 2015 - Future Science
Long mate pair (LMP) or “jump” libraries are invaluable for producing contiguous genome
assemblies and assessing structural variation. However the consistent production of high …

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

KA Hodgkinson, J Wright, GG Accinelli, D Heavens… - bioRxiv, 2022 - biorxiv.org
Fragilariopsis cylindrus CCMP1102 is characterised by a complex genome with significant
levels of heterozygosity between haplotypes, > 35% repeats, and an unknown karyotype. …

[HTML][HTML] A Sequence Distance Graph framework for genome assembly and analysis

L Yanes, GG Accinelli, J Wright, BJ Ward… - …, 2019 - ncbi.nlm.nih.gov
The Sequence Distance Graph (SDG) framework works with genome assembly graphs and
raw data from paired, linked and long reads. It includes a simple deBruijn graph module, and …