Zhao Kai's repositories
GFF3toolkit
Python programs for processing GFF3 files
3d-dna
3D de novo assembly (3D DNA) pipeline
allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
ASTRAL
Accurate Species TRee ALgorithm
ATACProc
ATAC-seq processing pipeline
blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
canu
A single molecule sequence assembler for genomes large and small.
Cogent
Coding Genome Reconstruction using Iso-Seq data
GWA_tutorial
A comprehensive tutorial about GWAS and PRS
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
iced
Normalizing Hi-C contact counts efficiently
IsoCon_Eval
Evaluation scripts for IsoCon + targeted sequencing approach
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Juicer-Docker
Docker for Juicer
LACHESIS
The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
Motrix
A full-featured download manager.
NOVOPlasty
NOVOPlasty - The organelle assembler and heteroplasmy caller
OrthoFinder
Phylogenetic orthology inference for comparative genomics
seqtk
Toolkit for processing sequences in FASTA/Q formats
transcriptx
autommated annotation pipeline for whole-transcriptome assemblies
trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
wgd
Python package and CLI for whole-genome duplication related analyses