whole-genome-sequencing

There are 111 repositories under whole-genome-sequencing topic.

  • nf-core/sarek

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

    Language:Nextflow413136728417

  • flowhub-team/WholeGenomeSequencing-WGS

    Whole Genome Sequencing analysis, WGS analysis

    24143052

  • ShujiaHuang/ilus

    A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

    Language:Python13051035

  • nanoporetech/pipeline-structural-variation

    Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

    Language:Python114282217

  • xihaoli/STAAR

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

    Language:C++91251742

  • TimD1/vcfdist

    vcfdist: Accurately benchmarking phased variant calls

    Language:C++796337

  • quinlan-lab/STRling

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

    Language:Nim637499

  • xihaoli/STAARpipeline

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

    Language:R6182120

  • BU-ISCIII/plasmidID

    PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

    Language:Shell384248

  • KCCG/mity

    mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

    Language:Python364283

  • jlumpe/gambit

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

    Language:Python29114

  • hw538/cfDNAPro

    cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

    Language:R28642

  • IARCbioinfo/alignment-nf

    Whole Exome/Whole Genome Sequencing alignment pipeline

    Language:Nextflow2851214

  • xihaoli/STAARpipeline-Tutorial

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

    Language:R2797217

  • edgardomortiz/Captus

    Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

    Language:Python236175

  • astrazeneca-cgr-publications/JARVIS

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

    Language:HTML22546

  • xihaoli/MetaSTAAR

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

    Language:R21677

  • ctmrbio/BACTpipe

    BACTpipe: An assembly and annotation pipeline for bacterial genomics

    Language:Groovy2051247

  • USDA-VS/vSNP

    vSNP -- validate SNPs

    Language:Python1971112

  • OpenOmics/genome-seek

    Clinical Whole Genome and Exome Sequencing Pipeline

    Language:Python1811911

  • pblaney/mgp1000

    Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

    Language:Nextflow11304

  • aryarm/as_analysis

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

    Language:R102769

  • kstawiski/seq-pipeline

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

    Language:PHP10101

  • rwk-unil/sapphire

    Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)

    Language:C++9221

  • xihaoli/STAARpipelineSummary

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

    Language:R9605

  • NadjaKry/WGS_pipeline

    Bacterial whole genome sequencing (WGS) analysis

    Language:Shell8202

  • rx32940/BactPrep

    Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)

    Language:Python8211

  • KiranJavkar/PRAWNS

    PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features

    Language:C++7141

  • USDA-VS/vSNP3

    vSNP -- validate SNPs

    Language:Python7291

  • christacaggiano/ENCODE_WGBS

    a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.

    Language:Python6402

  • imanyass/ShigaPass

    An in silico tool to predict Shigella serotypes

    Language:Shell6333

  • tobiasrausch/covid19

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

    Language:Python6431

  • KrasnitzLab/RAIDS

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

    Language:R52184

  • phansol/gremlin

    GREMLIN: Genomic REarrangements by Machine Learning-based INspection

    Language:R5101

  • supermaxiste/ARPEGGIO

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

    Language:Python53730

  • zjnolen/PopGLen

    Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

    Language:Python51140