An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

(2019) Wai Yee Low et al.   Nature Communications

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A continuous genome assembly of the corkwing wrasse ( Symphodus melops )

(2018) Morten Mattingsdal et al.   GENOMICS

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains

(2018) Emily J. Shields et al.   Cell Reports

Improved Genome Assembly and Annotation for the Rock Pigeon ( Columba livia )

(2018) Carson Holt et al.   G3-Genes Genomes Genetics

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo

(2018) Mian Xia et al.   GigaScience

How complete are “complete” genome assemblies?-An avian perspective

(2018) Valentina Peona et al.   Molecular Ecology Resources

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

(2018) Robert VanBuren et al.   GigaScience

Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

(2018) Lei Zhang et al.   Horticulture Research

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis

(2018) Diana Domanska et al.   BMC BIOINFORMATICS

Improved reference genome of Aedes aegypti informs arbovirus vector control

(2018) Benjamin J. Matthews et al.   NATURE

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

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

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

(2017) Patrick P Edger et al.   GigaScience

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

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

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

Brain/MINDS: A Japanese National Brain Project for Marmoset Neuroscience

(2016) Hideyuki Okano et al.   NEURON

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis

(2015) Kengo Sato et al.   Scientific Reports

Common marmoset as a new model animal for neuroscience research and genome editing technology

(2014) Noriyuki Kishi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)

(2014) Xinxia Peng et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The common marmoset as a novel animal model system for biomedical and neuroscience research applications

(2012) Hideyuki Okano et al.   Seminars in Fetal & Neonatal Medicine

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Generating induced pluripotent stem cells from common marmoset (Callithrix jacchus) fetal liver cells using defined factors, including Lin28

(2010) Ikuo Tomioka et al.   GENES TO CELLS

Generation of transgenic non-human primates with germline transmission

(2009) Erika Sasaki et al.   NATURE