Sh1ne111

lme4GS

lme4 for Genomic Selection

HackersDelight

Code from the book "Hacker's Delight" by Henry S. Warren, Jr. (original and my own modifications).

Hackers-Delight

Code to accompany Hacker's Delight 2nd Edition by Henry S Warren. PS: Will have my notes etc when I go through it.

dbgwas

Github (trivial) mirror for https://gitlab.com/leoisl/dbgwas

mergesort-concurrent

merge sort on singly-linked list utilzing POSIX Thread

kvec.h

fork of kvec.h in https://github.com/attractivechaos/klib

libbf

:dart: Bloom filters for C++11

REINDEER

REINDEER REad Index for abuNDancE quERy

LINKVIEW2

DNA序列比对结果 可视化展示工具

blast

simple plotter able to handle big fastas/flatfiles

pyGenomeViz

A genome visualization python package for comparative genomics

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

paf2dotplot

Draw a dot plot from a paf alignment

BloomFilterTrie

An alignment-free, reference-free and incremental data structure for colored de Bruijn graph with application to pan-genome indexing.

mantis

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

kmercount

Simple kmer counter using Bloom filter and efficient hash function

Colocalization

Co-localization analysis between reference GWAS and eQTL summary statistics

Gene-level-statistical-colocalization

sample

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

IBSpy

Python library to identify Identical By State regions

SPLASH

c_std

Implementation of C++ standard libraries in C

HFKReads

An ultra-fast and efficient tool for high frequency kmer sequencing reads extraction

SV-STR

katcher

Extract aligned reads containing a set of k-mers

kmdiff

Differential k-mer analysis

Tutorial_pan_genomics

Guide through code for a Minimmap2 genome alignment and a seq-seq-pan pan-genome alignment with visualizations in R. The tutorial presents an example using two haplotypes of the optix locus in Heliconius butterflies.

pandagma

Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.

HiC_tools

A collection of tools for Hi-C data analysis

Manuscript_Code

Repository for code used for publications