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Xuelei Dai's Projects

dsuite icon dsuite

Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

edta icon edta

Extensive de-novo TE Annotator

eqtlhap icon eqtlhap

eQTLHap: a comprehensive eQTL analysis tool.

findtelomeres icon findtelomeres

A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files

flye icon flye

De novo assembler for single molecule sequencing reads using repeat graphs

ggplot2 icon ggplot2

An implementation of the Grammar of Graphics in R

gnomix icon gnomix

A fast, scalable, and accurate local ancestry method.

graphtyper icon graphtyper

Population-scale genotyping using pangenome graphs

hal icon hal

Hierarchical Alignment Format

haplex icon haplex

Combinatorial and statistical prediction of gene expression from haplotype sequence

haplotype-resolved-potato-genome icon haplotype-resolved-potato-genome

The pipelines were built in the project resolving the genome of a diploid potato. Most of the scripts were sepcially designed to perform the analyses in the paper 'Haplotype-resolved genome analyses of a heterozygous diploid potato' (under review).

hic-pro icon hic-pro

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

hicplotter icon hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

hifiasm icon hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

isoseq icon isoseq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

isoseq_sa3nup icon isoseq_sa3nup

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

jcvi icon jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

juicebox icon juicebox

Visualization and analysis software for Hi-C data -

juicer icon juicer

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

loter icon loter

A software package for local ancestry inference and haplotype phasing

lumpy-sv icon lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

makehub icon makehub

Fully automated generation of UCSC assembly hubs

manta icon manta

Structural variant and indel caller for mapped sequencing data

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