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

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Definition of the Cattle Killer Cell Ig–like Receptor Gene Family: Comparison with Aurochs and Human Counterparts

(2014) Nicholas D. Sanderson et al.   JOURNAL OF IMMUNOLOGY

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Design and Characterization of a 52K SNP Chip for Goats

(2014) Gwenola Tosser-Klopp et al.   PLoS One

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

A whole-genome radiation hybrid panel for goat

(2012) X.Y. Du et al.   SMALL RUMINANT RESEARCH

Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

(2011) Jun Zhou et al.   Genome Biology and Evolution

Rapid whole genome optical mapping of Plasmodium falciparum

(2011) Matthew C Riley et al.   MALARIA JOURNAL

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The sheep genome reference sequence: a work in progress

(2010) et al.   ANIMAL GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

(2010) L Pérez-Pardal et al.   HEREDITY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

(2009) A. Barriere et al.   GENOME RESEARCH

Q-band karyotype of the goat (Capra hircus) and the relation between goat and bovine Q-bands

(2009) K. M. HANSEN   HEREDITAS

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

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

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

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

(2008) N. Nagarajan et al.   BIOINFORMATICS

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

(2008) S. Naderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY