An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)

Chromosomal Rearrangements during Turtle Evolution Altered the Synteny of Genes Involved in Vertebrate Sex Determination

(2019) LingSze Lee et al.   CYTOGENETIC AND GENOME RESEARCH

Genetic variation and admixture of red-eared sliders (Trachemys scripta elegans) in the USA

(2019) James F. Parham et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring synteny between genome assemblies: a systematic evaluation

(2018) Dang Liu et al.   BMC BIOINFORMATICS

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

(2018) Lauren Coombe et al.   BMC BIOINFORMATICS

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Assembly scaffolding with PE-contaminated mate-pair libraries

(2016) Kristoffer Sahlin et al.   BIOINFORMATICS

Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes

(2016) Eugenia E. Montiel et al.   CYTOGENETIC AND GENOME RESEARCH

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

NxTrim: optimized trimming of Illumina mate pair reads: Table 1.

(2015) Jared O’Connell et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

BESST - Efficient scaffolding of large fragmented assemblies

(2014) Kristoffer Sahlin et al.   BMC BIOINFORMATICS

Sex Determination: Why So Many Ways of Doing It?

(2014) Doris Bachtrog et al.   PLOS BIOLOGY

Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers

(2013) James F. Parham et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE