shehongbing's repositories
quarTeT
A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
pyrho
Fast inference of fine-scale recombination rates based on fused-LASSO
deepconsensus
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
transanno
accurate LiftOver tool for new genome assemblies
VCF2Dis
VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format
CAFE5
Version 5 of the CAFE phylogenetics software
TEsorter
TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
phasebook
Haplotype aware de novo assembly of diploid genome from long reads
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
TIP_finder
TIP_finder: Transposable element Insertion Polymorphism Finder for huge genomic datasets
vg
tools for working with genome variation graphs
EDTA
Extensive de-novo TE Annotator
PiGBS_Pipeline
Parent-independent genotyping of diploid potato
SNAP
Gene prediction software
svmu
A program to call variants from genome alignment
SPLITREADER
Split-read pipeline for the identification of non-reference TE insertions with TSDs
geneLift
Gene model transfer from closely related reference genomes using cDNA alignments
HuaSmallTools
Some bioinformic domestic scripts.
Unicycler
hybrid assembly pipeline for bacterial genomes