cmcshou's Stars
tk2/RetroSeq
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
LeileiCui/Dominance_3Stocks
Jwindler/AutoHiC
A novel genome assembly pipeline based on deep learning
shangshanzhizhe/Work_flow_of_population_genetics
整理常用的群体遗传学分析流程和脚本
Illumina/paragraph
Graph realignment tools for structural variants
PapenfussLab/sv_benchmark
Comprehensive benchmark of structural variant callers
jianlin-cheng/GenomeFlow
GenomeFlow: A Graphical Tool for Modeling and Analyzing 3D Genome Structure
DecodeGenetics/svimmer
Structural variant merging tool
pblischak/HyDe
Hybridization detection using phylogenetic invariants
TheFraserLab/ASEr
Get ASE counts from BAMs or raw fastq data -- repackage of pipeline by Carlo Artieri
shohei-kojima/MEGAnE
MEGAnE
PhyloSofS-Team/thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
fritzsedlazeck/SURVIVOR
Toolset for SV simulation, comparison and filtering
millanek/Dsuite
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
starskyzheng/panpop
Application of pan-genome for population
simonhmartin/genomics_general
General tools for genomic analyses.
ndierckx/NOVOPlasty
NOVOPlasty - The organelle assembler and heteroplasmy caller
bejerano-lab/percomorphCONDELs
ANGSD/angsd
Program for analysing NGS data.
baoxingsong/AnchorWave
Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
zeeev/smartie-sv
calling SVs from Blasr contig level alignments
MareesAT/GWA_tutorial
A comprehensive tutorial about GWAS and PRS
qiao-xin/DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
esayyari/DiscoVista
griffithlab/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.