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Starred repositories
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
A tool for quick and accurate calculation of syntenic diversity.
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
A genome completeness evaluation tool based on miniprot
Detecting differentially interacting genomic regions from Hi-C contact maps
Software for painlessly estimating average nucleotide diversity within and between populations
Experimental String Graph construction and processing
Tool for the Quality Control of Long-Read Defined Transcriptomes
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
A Python interface for PHAST (phylogenetic analysis with space/time models).
Tool for plotting sequencing data along genomic coordinates.
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
Accurate prediction of allele-specific gene expression (ASE) in hybrid poplar facilitated by a genome assembly
Cell age determination by scATAC-seq and bulk-ATAC-seq
Official home of genome aligner based upon notion of Cactus graphs
An efficient assembly tool for plant mitochondrial genome
Tools for improving the sensitivity and specificity of genome alignments
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
a software package for analysis of genetic association, Hardy-weinberg equilibrium, linkage disequilibrium and haplotype construction at multiallelic polymorphism loci, compatible for both diploid …