Hongwei Lu's repositories
3KRG-HAP
Haplotype marker based on 3,000 Rice Genomes for subpopulation inference
alphafold
Open source code for AlphaFold.
AnchorWave
sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
Badread
a long read simulator that can imitate many types of read problems
bamdst
a lightweight bam file depth statistical tool
ChatYuan
ChatYuan: Large Language Model for Dialogue in Chinese and English
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
EDTA
Extensive de-novo TE Annotator
GAAP
A genome assembly assessment pipeline.
GenePanGenomeByCollinearity
Pipeline to construct a gene-level pan genome with MCscan
genomescope
Fast genome analysis from unassembled short reads
GFA-spec
Graphical Fragment Assembly (GFA) Format Specification
graphtyper
Population-scale genotyping using pangenome graphs
localcolabfold
ColabFold on your local PC
MACS
MACS -- Model-based Analysis of ChIP-Seq
MoMI-G
Modular Multi-scale Integrated Genome Graph Browser
NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
NanoSim
Nanopore sequence read simulator
NLR-Annotator
NLR-Annotator upload
pbsim2
PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
plotsr
Tool to plot synteny and structural rearrangements between genomes
quast
Genome assembly evaluation tool
RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
scGENA
single cell Gene co-Expression Network Analysis
SURVIVOR
Toolset for SV simulation, comparison and filtering
thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
VCF2HAP
Construct gene haplotype with VCF format files and snpEff annotation.
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
WFA
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment