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awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

bxd_str_expand_prop_pub

Workflow and analyses scripts for: “A novel quantitative trait locus implicates Msh3 in genome-wide short tandem repeat expansion propensity in mice”

cattlegtex

The cattle Genotype-Tissue Expression atlas v1

chm13

The complete sequence of a human genome

cnview

Visualization and annotation of CNVs from population-scale whole-genome sequencing data

cpg

Building a Chinese pan-genome of 486 individuals

data-analysis-for-sds-in-t2t-chm13

Figures for the CHM13 T2T SD paper.

germline_mutation_rate

Pipeline to estimate germline mutation rate from NGS pedigree data

hic_tools

A collection of tools for Hi-C data analysis

i2qtl-sv-str-analysis

Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as part of the i2QTL consortium. This data set consists of sequencing data from the iPSCORE (Frazer lab) and HipSci projects.

iags

jasmine

Jasmine: SV Merging Across Samples

lorals_paper_code

marmoset

mutea

Python package to simulate and estimate Y-STR mutation models

nanopore-sv

The detection of structural variations in maize population

non-b_gfa

Identify non-B forming motifs

pear_haplotype_genome

Codes for pear haplotype genome and pangenome graph construction

piggtex-pipeline-v0

plotsr

Tool to plot synteny and structural rearrangements between genomes

soapdenovo2

Next generation sequencing reads de novo assembler.

sus_liver_estrs

Mapping short tandem repeats for liver gene expression traits help to prioritize potential causal variants for complex traits in pigs

sus_mevs_wgs

Mobile element variation contributes to population diversity and gene regulation in pigs

susrepeats

A repository of Sus scrofa short tandem repeats (STRs) project

sv-ont-tibetan

Characterization of Structural Variation in Chinese samples

sv-pipeline

Pipeline for structural variation detection in cohorts

t2t-variants

tmp_files

vg

tools for working with genome variation graphs

y-amplicon-evolution

Scripts used in Teitz et. al 2018