shehongbing

DNNGP

DNNGP: Deep neural network for genomic prediction

PseudogenePipeline

CAFE5

Version 5 of the CAFE phylogenetics software

cDNA_Cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

EDTA

Extensive de-novo TE Annotator

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

geneLift

Gene model transfer from closely related reference genomes using cDNA alignments

HuaSmallTools

Some bioinformic domestic scripts.

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

merqury

k-mer based assembly evaluation

My-script

myscripts

phasebook

Haplotype aware de novo assembly of diploid genome from long reads

PiGBS_Pipeline

Parent-independent genotyping of diploid potato

public

pyrho

Fast inference of fine-scale recombination rates based on fused-LASSO

quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

sexPhase

SNAP

Gene prediction software

SPLITREADER

Split-read pipeline for the identification of non-reference TE insertions with TSDs

SV

svmu

A program to call variants from genome alignment

TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

TIP_finder

TIP_finder: Transposable element Insertion Polymorphism Finder for huge genomic datasets

transanno

accurate LiftOver tool for new genome assemblies

Unicycler

hybrid assembly pipeline for bacterial genomes

VCF2Dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

vg

tools for working with genome variation graphs