ALLMAPS: robust scaffold ordering based on multiple maps

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

(2014) Wataru Kai et al.   BMC GENOMICS

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

High-coverage sequencing and annotated assemblies of the budgerigar genome

(2014) Ganeshkumar Ganapathy et al.   GigaScience

Toward a statistically explicit understanding of de novo sequence assembly

(2013) M. Howison et al.   BIOINFORMATICS

FPSAC: fast phylogenetic scaffolding of ancient contigs

(2013) Ashok Rajaraman et al.   BIOINFORMATICS

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

(2013) Sanjeev Kumar Sharma et al.   G3-Genes Genomes Genetics

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

(2012) Nian Wang et al.   BMC PLANT BIOLOGY

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

(2012) Yi Ren et al.   PLoS One

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

Two-Phase Analysis in Consensus Genetic Mapping

(2012) Y. Ronin et al.   G3-Genes Genomes Genetics

Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

(2011) J. W. VAN OOIJEN   Genetics Research

Dynamo maker ready to roll

(2011) Susan Young   NATURE

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

R/qtl: high-throughput multiple QTL mapping: Fig. 1.

(2010) Danny Arends et al.   BIOINFORMATICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A Single Molecule Scaffold for the Maize Genome

(2009) Shiguo Zhou et al.   PLoS Genetics

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

(2008) N. Nagarajan et al.   BIOINFORMATICS

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics