Works cited by this work

63 works

Work: Whole genome sequencing of Castanea mollissima and molecular mechanisms of sugar and starch synthesis

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian‐Jun Jin, Wen-Bin Yu, Jun-Bo Yang +4
Article202041 citations
ABI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love, Wolfgang Huber, Simon Anders
Article201414 citations
ABI
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred Grabherr, Brian J. Haas, Moran Yassour +18
Article201114 citations
ABI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Z. Yang
Article200711 citations
ABI
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis +2
Article201510 citations
ABI
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder, Steve Horvath
Article20089 citations
ABI
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu, Li-Gen Wang, Yanyan Han +1
Article20128 citations
ABI
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Mihaela Pertea, Geo Pertea, Corina Antonescu +3
Article20157 citations
ABI
CD-HIT: accelerated for clustering the next-generation sequencing data
LiMin Fu, Beifang Niu, Zhengwei Zhu +2
Article20127 citations
ABI
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Yupeng Wang, Haibao Tang, Jeremy D. DeBarry +9
Article20127 citations
ABI
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Todd M. Lowe, Sean R. Eddy
Article19977 citations
ABI
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng +2
Article20217 citations
ABI
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim, Ben Langmead, Steven L. Salzberg
Article20157 citations
ABI
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas, Steven L. Salzberg, Wei Zhu +6
Article20086 citations
ABI
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Brian Haas
Article20036 citations
ABI
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
Article20185 citations
ABI
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
Heng Li
Preprint20135 citations
ABI
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
Olga Dudchenko, Sanjit Singh Batra, Arina D. Omer +8
Article20174 citations
ABI
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
Pengchuan Sun, Beibei Jiao, Yongzhi Yang +6
Article20224 citations
ABI
DNA sequencing with chain-terminating inhibitors
Frederick Sanger, S. Nicklen, Alan Coulson
Article19774 citations
ABI
NextPolish: a fast and efficient genome polishing tool for long-read assembly
Jiang Hu, Junpeng Fan, Zongyi Sun +1
Article20193 citations
ABI
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Mario Stanke, Mark Diekhans, Robert Baertsch +1
Article20083 citations
ABI
Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Yu Xing, Yang Liu, Qing Zhang +10
Article20193 citations
ABI
Coming of age: ten years of next-generation sequencing technologies
Sara Goodwin, John D. McPherson, W. Richard McCombie
Review article20163 citations
ABI
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Other2 citations
ABI

Works cited by this work

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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

PAML 4: Phylogenetic Analysis by Maximum Likelihood

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

WGCNA: an R package for weighted correlation network analysis

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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

CD-HIT: accelerated for clustering the next-generation sequencing data

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

HISAT: a fast spliced aligner with low memory requirements

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

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Minimap2: pairwise alignment for nucleotide sequences

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

De novo assembly of the <i>Aedes aegypti</i> genome using Hi-C yields chromosome-length scaffolds

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

DNA sequencing with chain-terminating inhibitors

NextPolish: a fast and efficient genome polishing tool for long-read assembly

Using native and syntenically mapped cDNA alignments to improve <i>de novo</i> gene finding

Hybrid <i>de novo</i> genome assembly of Chinese chestnut (<i>Castanea mollissima</i>)

Coming of age: ten years of next-generation sequencing technologies

Untitled