whole-exome-sequencing

Here are 45 public repositories matching this topic...

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Updated Oct 30, 2024
Nextflow

xihaoli / STAARpipeline

Star

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

statistical-genetics whole-exome-sequencing whole-genome-sequencing functional-annotation rare-variant-analysis staar-pipeline

Updated Oct 25, 2024
R

IARCbioinfo / alignment-nf

Star

Whole Exome/Whole Genome Sequencing alignment pipeline

nextflow ngs gatk alignment bwa whole-exome-sequencing whole-genome-sequencing

Updated Sep 18, 2024
Nextflow

xihaoli / STAARpipeline-Tutorial

Star

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

statistical-genetics whole-exome-sequencing whole-genome-sequencing functional-annotation multi-trait-analysis rare-variant-analysis staar-pipeline

Updated Jul 26, 2024
R

OpenOmics / genome-seek

Star

Clinical Whole Genome and Exome Sequencing Pipeline

quality-control snakemake pipeline somatic-variants singularity copy-number-variation whole-exome-sequencing whole-genome-sequencing variant-annotation hla-typing germline-variants variant-effect-prediction structural-variants

Updated Nov 5, 2024
Python

luoyuanlab / autism_precision_medicine

Star

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

machine-learning rna-seq genomics graph-algorithms parallel-computing omics whole-exome-sequencing insurance-claims ehr-data

Updated Aug 11, 2020
Shell

kstawiski / seq-pipeline

Star

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

docker data-science machine-learning data-mining rna-seq pipeline rstudio vscode jupyter-notebook workspace whole-exome-sequencing whole-genome-sequencing smrna-seq

Updated Aug 25, 2023
PHP

xihaoli / STAARpipelineSummary

Star

An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies generated by STAARpipeline

statistical-genetics whole-exome-sequencing whole-genome-sequencing functional-annotation rare-variant-analysis staar-pipeline

Updated Oct 16, 2024
R

alexcoppe / iWhale

Star

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

docker bioinformatics snps genomics biology tumor indels whole-exome-sequencing scons

Updated May 27, 2020
Python

Vicellken / Whole_exome_sequence

Star

python pipeline shellscript whole-exome-sequencing gatk4

Updated Aug 29, 2019
Shell

jeongu / Cancer-Vaccine-Pipeline

Star

Constructing Neoantigen Vaccine Pipeline with pVACtools

rna-sequencing whole-exome-sequencing pvac-seq cancer-immunotherapy

Updated May 12, 2019
Shell

LOVDnl / LOVDplus

Star

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

ngs whole-exome-sequencing variant-analysis ngs-analysis variant-interpretation lovd

Updated Jun 4, 2024
PHP

CCBR / Pipeliner

Star

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

quality-control rna-seq chip-seq whole-exome-sequencing whole-genome-sequencing single-cell-rna-seq mirna-seq

Updated Jul 13, 2023
Python

li-lab-genetics / staarpipeline-rap

Star

An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP

statistical-genetics whole-exome-sequencing whole-genome-sequencing functional-annotation staar-pipeline

Updated Jun 30, 2024
R

mehdimerbah / WES

Star

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

quality variants whole-exome-sequencing ngs-pipeline fastqc trimmomatic quality-scores tile-quality

Updated Apr 2, 2022
HTML

genomicsITER-developers / wdl

Star

WDL-based pipelines

workflow bioinformatics pipeline gatk wdl whole-exome-sequencing whole-genome-sequencing

Updated Jul 6, 2021
WDL

li-lab-genetics / favorannotator-rap

Star

An app for automatically functionally annotating the variants of whole-genome/whole-exome sequencing (WGS/WES) studies and integrating the functional annotations with the genotype data using FAVORannotator in UK Biobank RAP

whole-exome-sequencing whole-genome-sequencing functional-annotation favor-annotator