Pinned Repositories
3d-dna
3D de novo assembly (3D DNA) pipeline
AliTV-perl-interface
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
GFF3toolkit
Python programs for processing GFF3 files
zhaokai2014's Repositories
zhaokai2014/GFF3toolkit
Python programs for processing GFF3 files
zhaokai2014/3d-dna
3D de novo assembly (3D DNA) pipeline
zhaokai2014/AliTV-perl-interface
zhaokai2014/allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
zhaokai2014/ASTRAL
Accurate Species TRee ALgorithm
zhaokai2014/ATACProc
ATAC-seq processing pipeline
zhaokai2014/blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
zhaokai2014/CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
zhaokai2014/canu
A single molecule sequence assembler for genomes large and small.
zhaokai2014/Cogent
Coding Genome Reconstruction using Iso-Seq data
zhaokai2014/GWA_tutorial
A comprehensive tutorial about GWAS and PRS
zhaokai2014/HaploMerger2
zhaokai2014/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
zhaokai2014/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
zhaokai2014/iced
Normalizing Hi-C contact counts efficiently
zhaokai2014/IRscope
zhaokai2014/IsoCon_Eval
Evaluation scripts for IsoCon + targeted sequencing approach
zhaokai2014/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
zhaokai2014/Juicer-Docker
Docker for Juicer
zhaokai2014/LACHESIS
The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
zhaokai2014/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.
zhaokai2014/Motrix
A full-featured download manager.
zhaokai2014/NOVOPlasty
NOVOPlasty - The organelle assembler and heteroplasmy caller
zhaokai2014/OrthoFinder
Phylogenetic orthology inference for comparative genomics
zhaokai2014/seqtk
Toolkit for processing sequences in FASTA/Q formats
zhaokai2014/transcriptx
autommated annotation pipeline for whole-transcriptome assemblies
zhaokai2014/trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
zhaokai2014/wgd
Python package and CLI for whole-genome duplication related analyses