Integrative analysis of 111 reference human epigenomes
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Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
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ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide
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Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
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Indexing Graphs for Path Queries with Applications in Genome Research
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HISAT: a fast spliced aligner with low memory requirements
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The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities
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ChromHMM: automating chromatin-state discovery and characterization
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Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
10.1093/nar/gky504 · doi-reference
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
10.1093/bioinformatics/btt656 · doi-reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
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Synteny and Collinearity in Plant Genomes
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GFF Utilities: GffRead and GffCompare
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A complete bacterial genome assembled de novo using only nanopore sequencing data
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New strategies to improve minimap2 alignment accuracy
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Model-based Analysis of ChIP-Seq (MACS)
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BEDTools: a flexible suite of utilities for comparing genomic features
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Sambamba: fast processing of NGS alignment formats
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Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
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Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization
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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
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Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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Genome Annotation and Curation Using MAKER and MAKER-P
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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De novo reconstruction of satellite repeat units from sequence data
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RepeatModeler2 for automated genomic discovery of transposable element families
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
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Fast and accurate de novo genome assembly from long uncorrected reads
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
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Heterochromatin: did H3K9 methylation evolve to tame transposons?
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H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction
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Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance
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Near telomere-to-telomere genome assemblies of Silkie Gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds
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A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
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The complete genome of a songbird
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Chromosome-level genome assembly of the European green woodpecker Picus viridis
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A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species
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