The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies

The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies

(2019) Baohua Chen et al.   Scientific Data

Transcriptional differences provide insight into environmental acclimatization in wild amur ide (Leuciscus waleckii) during spawning migration from alkalized lake to freshwater river

(2018) Baohua Chen et al.   GENOMICS

Draft genome of the Northern snakehead, Channa argus

(2017) Jian Xu et al.   GigaScience

Comparison of growth parameters of tiger puffer Takifugu rubripes from two culture systems in China

(2016) Qing-Lin Wang et al.   AQUACULTURE

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscuswaleckii) in an Extremely Alkaline Environment

(2016) Jian Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

(2016) Wenzhu Peng et al.   Scientific Reports

The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

(2016) Hailin Pan et al.   GigaScience

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

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki 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

Genome assembly and haplotyping with Hi-C

(2013) Jan O Korbel et al.   NATURE BIOTECHNOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals

(2011) Wataru Kai et al.   Genome Biology and Evolution

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY