Projects in Awesome Lists tagged with whole-genome-sequencing

https://github.com/nf-core/sarek

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

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 11 Apr 2025

https://github.com/shujiahuang/ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

bioinformatics bioinformatics-pipeline pipeline variant-calling whole-genome-sequencing workflow-management

Last synced: 12 Apr 2025

https://github.com/quinlan-lab/strling

Detect novel (and reference) STR expansions from short-read data

hacktoberfest nim-lang short-tandem-repeats str whole-genome-sequencing

Last synced: 09 Apr 2025

https://github.com/jlumpe/gambit

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

bioinformatics genomics microbiology public-health whole-genome-sequencing

Last synced: 10 Apr 2025

https://github.com/astrazeneca-cgr-publications/jarvis

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes

deeplearning genomics non-coding-variants tensorflow whole-genome-sequencing

Last synced: 10 Apr 2025

https://github.com/astrazeneca-cgr-publications/JARVIS

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes

deeplearning genomics non-coding-variants tensorflow whole-genome-sequencing

Last synced: 18 Jan 2025

https://github.com/aryarm/as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

allele-specific-expression atac-seq rna-seq snakemake whole-genome-sequencing

Last synced: 11 Apr 2025

https://github.com/tobiasrausch/covid19

SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing

consensus covid19 covid19-analysis sars-cov-2 variant-calling whole-genome-sequencing

Last synced: 13 Apr 2025

https://github.com/krasnitzlab/raids

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

ancestry cancer-genomics exome-sequencing genomics inference r-language r-package rna-seq rna-sequencing whole-genome-sequencing

Last synced: 12 Apr 2025

https://github.com/supermaxiste/arpeggio

A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

allopolyploid automation bisulfite-sequencing dna-methylation epigenetics plants reproducibility snakemake whole-genome-sequencing workflow

Last synced: 17 Mar 2025

https://github.com/sdhutchins/vcf-prepping

Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

bcftools exome-sequencing vcf wgs whole-genome-sequencing

Last synced: 08 Apr 2025

https://github.com/leahkemp/test_sv_callers

Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).

illumina structural-variants whole-genome-sequencing

Last synced: 27 Feb 2025

https://github.com/laura-budurlean/structural_variant_discovery

A combination of optical genome mapping with Bionano and whole genome sequencing short-read data. This pipeline was created to help integrate structural variant calling from these two technologies.

bionano optical-genome-mapping optical-mapping structural-variation structural-variation-calling sv-calling wgs whole-genome-sequencing