ChaissonLab

LRA

Long read aligner

vamos

VNTR annotation using motif selection

danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction

hmcnc

Hidden Markov Model based Copy number caller

TT-Mars

Structural Variants Assessment Based on Haplotype-resolved Assemblies

SegDupAnnotation

SegDupAnnotation2

Count gene duplications.

CARD-VNTR

Tandem repeat analysis for the CARD consortium

devas

Deep learning validation of SV calls

AssemblyAnalysis

chaissonlab.github.io

Start page for lab website.

danbing-tk_rxiv

Genome-wide genotyping of VNTRs from short-read datasets with haplotype-resolved database

eMotif_manuscript_analysis_scripts

Analysis scripts associated with the manuscript "The motif composition of variable-number tandem repeats impacts gene expression", including bias correction, eQTL mapping, fine-mapping, and genome folding prediction.

GenomeIndex

paths to genome data -> download

hgsvg

Analysis code for 1kg

PartitionedAssembly

Simple phase partitioned pipeline

rare-var-scratch

ScreenInversions

Simple code to look for inversions in local assemblies.

sedef

Identification of segmental duplications in the genome

vamos-somatic

A wdl file for generating per-read calls for tandem repeats in long-read data.

bioconda-recipes

Conda recipes for the bioconda channel.

Ctyper

Genotyping of paralog specific gene types

GTEx-tools

Small tool-list for gtex

mcst

Simple sam manipulation code. Includes inversion finding.

RepeatMasking

A snakefile to run repeatmasker on genomes in a scatter/gather approach.