Genome sequencing and population genomics in non-model organisms

H Ellegren - Trends in ecology & evolution, 2014 - cell.com
High-throughput sequencing technologies are revolutionizing the life sciences. The past 12
months have seen a burst of genome sequences from non-model organisms, in each case …

A field guide to whole‐genome sequencing, assembly and annotation

R Ekblom, JBW Wolf - Evolutionary applications, 2014 - Wiley Online Library
Genome sequencing projects were long confined to biomedical model organisms and
required the concerted effort of large consortia. Rapid progress in high‐throughput …

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

M Alonge, S Soyk, S Ramakrishnan, X Wang… - Genome biology, 2019 - Springer
We present RaGOO, a reference-guided contig ordering and orienting tool that leverages
the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies …

Earth BioGenome Project: Sequencing life for the future of life

HA Lewin, GE Robinson, WJ Kress… - Proceedings of the …, 2018 - National Acad Sciences
Increasing our understanding of Earth's biodiversity and responsibly stewarding its
resources are among the most crucial scientific and social challenges of the new …

Comparative genomics reveals insights into avian genome evolution and adaptation

G Zhang, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz… - Science, 2014 - science.org
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance
across many research fields. We explored bird macroevolution using full genomes from 48 …

The Genome 10K Project: a way forward

KP Koepfli, B Paten… - Annu. Rev. Anim …, 2015 - annualreviews.org
The Genome 10K Project was established in 2009 by a consortium of biologists and
genome scientists determined to facilitate the sequencing and analysis of the complete …

How to identify sex chromosomes and their turnover

DH Palmer, TF Rogers, R Dean, AE Wright - Molecular ecology, 2019 - Wiley Online Library
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems
that control sex determination are highly variable. In many organisms the presence of sex …

MeDuSa: a multi-draft based scaffolder

E Bosi, B Donati, M Galardini, S Brunetti… - …, 2015 - academic.oup.com
Motivation: Completing the genome sequence of an organism is an important task in
comparative, functional and structural genomics. However, this remains a challenging issue …

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

A Bissett, A Fitzgerald, T Meintjes, PM Mele, F Reith… - GigaScience, 2016 - Springer
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …

Navigating microbiological food safety in the era of whole-genome sequencing

J Ronholm, N Nasheri, N Petronella… - Clinical microbiology …, 2016 - Am Soc Microbiol
The epidemiological investigation of a foodborne outbreak, including identification of related
cases, source attribution, and development of intervention strategies, relies heavily on the …