whole-genome-sequencing

There are 6 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
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing conda reproducible-research containers germline somatic variant-calling nf-core gatk4 annotation whole-genome-sequencing whole-exome-sequencing pre-processing target-panels
Language:Nextflow 333
flowhub-team / WholeGenomeSequencing-WGS
Whole Genome Sequencing analysis, WGS analysis
bioinfomatics bioinformatics-pipeline genome wes wgs whole-genome-sequencing
241
nanoporetech / pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
nanopore structural-variation whole-genome-sequencing long-reads
Language:Python 110
ShujiaHuang / ilus
A 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.
whole-genome-sequencing variant-calling bioinformatics bioinformatics-pipeline pipeline
Language:Python 105
xihaoli / STAAR
An R package for performing STAAR procedure in whole-genome sequencing studies
whole-genome-sequencing statistical-genetics staar-procedure functional-annotation rare-variant-analysis
Language:C++ 82
TimD1 / vcfdist
vcfdist: Accurately benchmarking phased variant calls
alignment genomics genomics-analysis variant-calling whole-genome-sequencing bioinformatics vcf
Language:C++ 63
quinlan-lab / STRling
Detect novel (and reference) STR expansions from short-read data
short-tandem-repeats str whole-genome-sequencing nim-lang hacktoberfest
Language:Nim 57
xihaoli / STAARpipeline
An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline
statistical-genetics whole-genome-sequencing whole-exome-sequencing functional-annotation rare-variant-analysis staar-pipeline
Language:R 50
BU-ISCIII / plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
plasmid ngs ngs-analysis microbiology whole-genome-sequencing
Language:Shell 36
KCCG / mity
mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
genomics bioinformatics mitochondria precision-medicine whole-genome-sequencing
Language:Python 34
IARCbioinfo / alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
nextflow gatk bwa alignment ngs whole-exome-sequencing whole-genome-sequencing
Language:Nextflow 25
hw538 / cfDNAPro
cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
cell-free-dna genomics-visualization swgs whole-genome-sequencing liquid-biopsy cancer-genomics cancer-research early-detection bioinformatics r
Language:R 22
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
Language:HTML 21
ctmrbio / BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
nextflow pipeline whole-genome-sequencing bacteria bioinformatics assembly annotation
Language:Groovy 20
jlumpe / gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
bioinformatics genomics microbiology public-health whole-genome-sequencing
Language:Python 20
xihaoli / MetaSTAAR
An R package for performing MetaSTAAR procedure in whole-genome sequencing studies
statistical-genetics whole-genome-sequencing meta-analysis functional-annotation rare-variant-analysis metastaar-procedure
Language:R 19
USDA-VS / vSNP
vSNP -- validate SNPs
snp pipeline genomics tuberculosis brucella analysis-pipeline mycobacterium-tuberculosis-complex snps whole-genome-sequencing high high-throughput-sequencing bam-files vcf phylogenetics freebayes wgs
Language:Python 18
xihaoli / STAARpipeline-Tutorial
The tutorial for performing 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 rare-variant-analysis staar-pipeline
Language:R 18
OpenOmics / genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
copy-number-variation germline-variants quality-control structural-variants singularity snakemake whole-genome-sequencing somatic-variants pipeline hla-typing variant-annotation variant-effect-prediction whole-exome-sequencing
Language:Python 14
edgardomortiz / Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
ngs phylogenomics alignment genome-skimming high-throughput-sequencing hybridization-capture next-generation-sequencing phylogenetics rna-seq whole-genome-sequencing phylotranscriptomics orthologs paralogs target-capture busco-lineages busco-orthologs bioinformatics
Language:Python 13
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.
data-mining data-science docker jupyter-notebook machine-learning pipeline rna-seq rstudio smrna-seq vscode whole-exome-sequencing whole-genome-sequencing workspace
Language:PHP 10
aryarm / as_analysis
A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
snakemake allele-specific-expression rna-seq atac-seq whole-genome-sequencing
Language:R 9
NadjaKry / WGS_pipeline
Bacterial whole genome sequencing (WGS) analysis
genomics whole-genome-sequencing microbiology bioinformatics
Language:Shell 8
pblaney / mgp1000
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
bioinformatics cancer genomics germline nextflow pipeline preprocessing somatic variant-calling whole-genome-sequencing
Language:Nextflow 8
rwk-unil / sapphire
Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)
genetics genomics haplotypecaller haplotypes whole-genome-sequencing
Language:C++ 8
rx32940 / BactPrep
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
bacterial-genomes pangenome snakemake whole-genome-sequencing
Language:Python 8
xihaoli / STAARpipelineSummary
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-genome-sequencing whole-exome-sequencing functional-annotation rare-variant-analysis staar-pipeline
Language:R 8
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
population-genomics comparative-genomics whole-genome-genotyping pan-genome-analysis bioinformatics genomics computational-biology antimicrobial-resistance bacterial-gwas antibiotic-resistance whole-genome-sequencing whole-genome-alignment genome-analysis parallel-programming association-studies microbial-genomics
Language:C++ 7
tobiasrausch / covid19
SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing
sars-cov-2 covid19 covid19-analysis variant-calling consensus whole-genome-sequencing
Language:Python 6
christacaggiano / ENCODE_WGBS
a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.
whole-genome-sequencing bisulfite-sequencing bioinformatics
Language:Python 5
KrasnitzLab / RAIDS
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
ancestry inference genomics r-language r-package whole-genome-sequencing rna-sequencing rna-seq exome-sequencing cancer-genomics
Language:R 5
phansol / gremlin
GREMLIN: Genomic REarrangements by Machine Learning-based INspection
cancer-genomics structural-variation whole-genome-sequencing bioinformatics
Language:R 5
supermaxiste / ARPEGGIO
A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.
snakemake bisulfite-sequencing plants allopolyploid reproducibility automation workflow dna-methylation whole-genome-sequencing epigenetics
Language:Python 5
CCBR / Pipeliner
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
rna-seq whole-genome-sequencing whole-exome-sequencing single-cell-rna-seq mirna-seq quality-control chip-seq
Language:Python 4
li-lab-genetics / staarpipeline-rap
An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP
functional-annotation staar-pipeline statistical-genetics whole-exome-sequencing whole-genome-sequencing
Language:R 3
xihaoli / MultiSTAAR
An R package for performing MultiSTAAR procedure in whole-genome sequencing studies
functional-annotation multi-trait-analysis multistaar-procedure rare-variant-analysis statistical-genetics whole-genome-sequencing
Language:R 3