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 …

Sequencing technologies—the next generation

ML Metzker - Nature reviews genetics, 2010 - nature.com
Demand has never been greater for revolutionary technologies that deliver fast, inexpensive
and accurate genome information. This challenge has catalysed the development of next …

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

N Dierckxsens, P Mardulyn, G Smits - Nucleic acids research, 2017 - academic.oup.com
The evolution in next-generation sequencing (NGS) technology has led to the development
of many different assembly algorithms, but few of them focus on assembling the organelle …

The cityscapes dataset for semantic urban scene understanding

M Cordts, M Omran, S Ramos… - Proceedings of the …, 2016 - openaccess.thecvf.com
Visual understanding of complex urban street scenes is an enabling factor for a wide range
of applications. Object detection has benefited enormously from large-scale datasets …

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

M Castellarin, RL Warren, JD Freeman… - Genome …, 2012 - genome.cshlp.org
An estimated 15% or more of the cancer burden worldwide is attributable to known
infectious agents. We screened colorectal carcinoma and matched normal tissue specimens …

Scaffolding pre-assembled contigs using SSPACE

M Boetzer, CV Henkel, HJ Jansen, D Butler… - …, 2011 - academic.oup.com
De novo assembly tools play a main role in reconstructing genomes from next-generation
sequencing (NGS) data and usually yield a number of contigs. Using paired-read …

De novo assembly of human genomes with massively parallel short read sequencing

R Li, H Zhu, J Ruan, W Qian, X Fang, Z Shi… - Genome …, 2010 - genome.cshlp.org
Next-generation massively parallel DNA sequencing technologies provide ultrahigh
throughput at a substantially lower unit data cost; however, the data are very short read …

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

SA Bustin, V Benes, JA Garson, J Hellemans, J Huggett… - 2009 - academic.oup.com
Background: Currently, a lack of consensus exists on how best to perform and interpret
quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of …

ABySS: a parallel assembler for short read sequence data

JT Simpson, K Wong, SD Jackman, JE Schein… - Genome …, 2009 - genome.cshlp.org
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing
instruments has prompted the recent development of de novo short read assembly …

Next-generation DNA sequencing

J Shendure, H Ji - Nature biotechnology, 2008 - nature.com
DNA sequence represents a single format onto which a broad range of biological
phenomena can be projected for high-throughput data collection. Over the past three years …