Hongwei Lu's repositories
thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GenePanGenomeByCollinearity
Pipeline to construct a gene-level pan genome with MCscan
Augustus_train
Augustus Train pipline
ggheatmap
ggplot2 version of heatmap
bsa
Bulked-Segregant Analysis using vcf file with or without parents
networkx
Network Analysis in Python
Contig2Chr_ByRef
mapping contig to chr and link the contig to chr by mapping result
MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
syri
Synteny and Rearrangement Identifier
python-apollo
Python library for talking to Apollo API
flo
Same species annotation lift over pipeline.
dspr-asm
Contains scripts and programs used to generate assemblies and variants for the DSPR project
kent
UCSC Genome Browser source tree. Stable branch: "beta".
vg
tools for working with genome variation graphs
merqury
k-mer based assembly evaluation
cactus
Official home of genome aligner based upon notion of Cactus graphs
pgge
the pangenome graph evaluator
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
minigraph
Proof-of-concept seq-to-graph mapper and graph generator
neat-genreads
NEAT read simulation tools
BetaScan
Genome-wide scan for balancing selection using beta statistic
GSAlign
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
PopGen
Small scripts for population genetics analysis
Yleaf
Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data
isONcorrect
Error correction of ONT transcript reads