Zhao Kai (zhaokai2014)

zhaokai2014

Geek Repo

Company:FNU

Location:Fuzhou

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Zhao Kai's repositories

GFF3toolkit

Python programs for processing GFF3 files

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3d-dna

3D de novo assembly (3D DNA) pipeline

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allhic

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

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ASTRAL

Accurate Species TRee ALgorithm

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ATACProc

ATAC-seq processing pipeline

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blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

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CAFE

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

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canu

A single molecule sequence assembler for genomes large and small.

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Cogent

Coding Genome Reconstruction using Iso-Seq data

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GWA_tutorial

A comprehensive tutorial about GWAS and PRS

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HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

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hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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iced

Normalizing Hi-C contact counts efficiently

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IsoCon_Eval

Evaluation scripts for IsoCon + targeted sequencing approach

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juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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Juicer-Docker

Docker for Juicer

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LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

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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.

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Motrix

A full-featured download manager.

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NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller

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OrthoFinder

Phylogenetic orthology inference for comparative genomics

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seqtk

Toolkit for processing sequences in FASTA/Q formats

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transcriptx

autommated annotation pipeline for whole-transcriptome assemblies

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trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

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wgd

Python package and CLI for whole-genome duplication related analyses

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