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16gt

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

atac_seq_nmnat1

NMNAT1 Atac-seq data

cabana

CABANA is an intuitive visualization tool for copy number changes from NGS data. Core algorithms for academic researchers are available from GitHub (https://github.com/lstlab/CABANA), and for commercial use, please contact us ([email protected]).

cnv_wes_pipeline

cnv_wgs_pipeline

cwas

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dragen-gatk

Dragen-GATK pipeline for NGS mapping and variant calling

expansionhunter

A tool for estimating repeat sizes

gatk4-basic-joint-genotyping

Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.

gatk4-mitochondria-pipeline

This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

geneburdenrd

ird

kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

melt2docker

A ready to use docker image with a up and running MELT installation for genomic mobile elements discovery.

neural-enhance

Super Resolution for images using deep learning.

phenotips

PhenoTips provides an easy-to-use Web interface and standardized database back-end for collecting clinical findings observed in patients with possible genetic disorders.

preprocessing_hg38

retfound_mae

RETFound - A foundation model for retinal image

retrosom

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

rp1_aluinsertion

sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

spark

Publication quality NGS track plotting

staar

An R package for performing STAAR procedure in whole-genome sequencing studies

sv-cnv-studies

Relevant papers for CNV and SV approaches

tiledb-vcf

Efficient variant-call data storage and retrieval library using the TileDB storage library.

wdl-bootcamp-jinuhan