Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes

(2018) David Thybert et al.   GENOME RESEARCH

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Direct determination of diploid genome sequences

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

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Simultaneous gene finding in multiple genomes

(2016) Stefanie König et al.   BIOINFORMATICS

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

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

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Identification of distinct genes associated with seawater aspiration-induced acute lung injury by gene expression profile analysis

(2016) Wei Liu et al.   Molecular Medicine Reports

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

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

The ExAC browser: displaying reference data information from over 60 000 exomes

(2016) Konrad J. Karczewski et al.   NUCLEIC ACIDS RESEARCH

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Gene expression defines natural changes in mammalian lifespan

(2015) Alexey A. Fushan et al.   AGING CELL

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

Current methods for automated annotation of protein-coding genes

(2015) KJ Hoff et al.   Current Opinion in Insect Science

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

Comparative assembly hubs: Web-accessible browsers for comparative genomics

(2014) Ngan Nguyen et al.   BIOINFORMATICS

Single haplotype assembly of the human genome from a hydatidiform mole

(2014) Karyn Meltz Steinberg et al.   GENOME RESEARCH

Alignathon: a competitive assessment of whole-genome alignment methods

(2014) Dent Earl et al.   GENOME RESEARCH

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

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

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS