GitHub topics: wgs

Repositories

nf-core/oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Language: Nextflow - Size: 6.62 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 80 - Forks: 24

As a tool for cancer subtype prediction, Keraon uses features derived from cell-free DNA (cfDNA) in conjunction with PDX reference models to perform both classification and heterogenous phenotype fraction estimation.

Language: Python - Size: 2.21 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 2

enormandeau/wgs_sample_preparation

Trim, Align to genome, Deduplicate, Realign WGS sequencing samples

Language: Shell - Size: 56.6 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 16 - Forks: 7

kylegontjes/phylogenetic-resistance-ms

Code, data, and results for the phylogenetic resistance manuscript

Language: HTML - Size: 70.4 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

AMRmicrobiology/WGS-Analysis-VariantCalling

Nextflow pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.

Language: Nextflow - Size: 937 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 3 - Forks: 0

igordot/sns

Analysis pipelines for genomic sequencing data

Language: Shell - Size: 542 KB - Last synced at: about 18 hours ago - Pushed at: about 20 hours ago - Stars: 69 - Forks: 27

Illumina/Cyrius

A tool to genotype CYP2D6 with WGS data

Language: Python - Size: 5.1 MB - Last synced at: 13 days ago - Pushed at: almost 2 years ago - Stars: 53 - Forks: 6

oschwengers/platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Language: Python - Size: 37.4 MB - Last synced at: 23 days ago - Pushed at: 8 months ago - Stars: 118 - Forks: 15

zhukovanadezhda/cnv-psychosis

🧬🔍CNV analysis and outcome prediction in Ultra-High-Risk and First Episode Psychosis individuals 🩺🧠

Language: Jupyter Notebook - Size: 8.29 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 1 - Forks: 1

sdegeorgia/LAAVA-summary

A comprehensive pipeline for detecting, characterizing, and visualizing recombinant AAV (rAAV) integration sites using Oxford Nanopore long-read sequencing data.

Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sdegeorgia/CANVAS-summary

CNV Analysis Next-gen Variant Assessment Suite

Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

zhengxwen/GDSAnnotator

Whole-genome variant annotation data manipulation using GDS files

Language: R - Size: 565 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

zhengxwen/SeqArray

Data management of large-scale whole-genome sequence variant calls using GDS files (Development version only)

Language: C++ - Size: 9.86 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 46 - Forks: 12

xvill/xutil

经纬度转换，sqlldr入库，Geometry工具

Language: Go - Size: 298 KB - Last synced at: 21 days ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 8

BU-ISCIII/bacterial_wgs_training

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

Language: HTML - Size: 166 MB - Last synced at: 18 days ago - Pushed at: 10 months ago - Stars: 4 - Forks: 0

oschwengers/tadrep

Targeted Detection and Reconstruction of Plasmids

Language: Python - Size: 2.63 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 1

plantinformatics/shortbread2

Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.

Language: Perl - Size: 819 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 1

oschwengers/referenceseeker

Rapid determination of appropriate reference genomes.

Language: Python - Size: 19.7 MB - Last synced at: about 2 hours ago - Pushed at: 8 months ago - Stars: 98 - Forks: 6

nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 187 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 103 - Forks: 46

13xforever/wgs-exporter

Export save data from Microsoft Store/Game Pass version of the games

Language: C# - Size: 5.86 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 0

Daylily-Informatics/daylily

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Language: Python - Size: 350 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 23 - Forks: 2

USDA-VS/vSNP3

vSNP -- validate SNPs

Language: Python - Size: 5.93 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 12 - Forks: 2

CCICB/nf-fastq2bam

Nextflow pipeline to convert FASTQ files to BAM for WGS and RNA-seq data

Language: Nextflow - Size: 225 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

senzhaocode/FuSViz

A web-browser app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

Language: JavaScript - Size: 86.9 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 10 - Forks: 4

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced at: 2 months ago - Pushed at: 12 months ago - Stars: 21 - Forks: 12

LLQ95/Practical-Encyclopedia-of-Whole-Genome-Analysis

Practical Encyclopedia of Whole Genome Sequencing Analysis

Size: 1.66 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

rintrgthb/Joy-bioinformatics-division

Contain projects in bioinformatics fields

Size: 672 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

tycheleturner/ElGenomaPequeno

El genoma pequeño - analysis workflow for "the little genome." This repository holds a computational workflow to analyze the mitochondrial genome.

Language: R - Size: 959 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 7 - Forks: 1

nf-core/pacvar

Longread PacBio sequencing processing for WGS and PureTarget

Language: Nextflow - Size: 345 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 10 - Forks: 6

laura-budurlean/PCA-Ethnicity-Determination-from-WGS-Data

A pipeline utilizing PCA on 1000 genomes and WGS data from your own samples to determine or validate ancestry of an individual.

Language: Shell - Size: 43 KB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 4 - Forks: 0

dmnfarrell/tracebtb

M.bovis WGS surveillance tool.

Language: Jupyter Notebook - Size: 47 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language: Nim - Size: 1.17 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 725 - Forks: 100

GooglingTheCancerGenome/sv-callers

Snakemake-based workflow for detecting structural variants in genomic data

Language: Python - Size: 210 MB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 80 - Forks: 35

aongithub172/recsalmo

Bioinformatics tool for Salmonella WGS analysis

Language: Python - Size: 9.08 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

GunzIvan28/rMAP

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

Language: Shell - Size: 6.27 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 22 - Forks: 17

fralonra/wgs

WGSL based pixel shader format that can run on native and Web.

Language: Rust - Size: 449 KB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

lucast122/MMonitor-old

Software for monitoring metagenomes using nanopore sequencing reads

Language: C - Size: 156 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

jlchen5/Copy-number-analysis

This shell script is for analysing the DNA copy number via WGS data

Language: Shell - Size: 9.77 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

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.

Language: Shell - Size: 15.9 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

arikw/itm-to-wgs84-converter

A Zero dependency ITM to WGS84 coordinates converter

Language: JavaScript - Size: 31.3 KB - Last synced at: 5 days ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

chiqors/WGS-Absence-Backend

WGS Absence Repository for Backend Services. Powered by ExpressJS, and PostgreSQL

Language: JavaScript - Size: 410 KB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

kkwock/VARify

Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts

Language: HTML - Size: 48.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/GermlineShortV_biovalidation

Workflow for biological validation of germline SNP and indel variant datasets.

Language: Shell - Size: 143 KB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

laura-budurlean/GATK-WGS-Pipeline

GATK WGS workflow

Language: Shell - Size: 10.7 KB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

nadar/swiss-coordinates

Converter for Swiss-Coordinates and WGS-Coordinates.

Language: PHP - Size: 4.88 KB - Last synced at: 22 days ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

chiqors/WGS-Absence-Frontend

WGS Absence Repository for Frontend Services. Powered by ReactJS with Google oAuth 2.0

Language: JavaScript - Size: 4.56 MB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

fralonra/wgs-player

WGS player for the Web

Language: TypeScript - Size: 1.01 MB - Last synced at: about 16 hours ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

CDCgov/bpertussis-ciwgs

Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️

Language: Nextflow - Size: 54.4 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 2 - Forks: 2

frichter/ore

Associate outliers with rare variation

Language: Python - Size: 150 MB - Last synced at: 7 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

czheluo/Env-pipeline

Bayesian method for Environmental correlations analysis pipeline

Language: Python - Size: 4.62 MB - Last synced at: 6 months ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0

chiqors/WGS-BootcampBatch5-AllRepositories 📦

All WGS Bootcamp Batch 5 Repositories

Language: JavaScript - Size: 364 KB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

io-sgr/geometry-common

Language: Java - Size: 142 KB - Last synced at: 12 days ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 1

cchd0001/GenomeSequenceSimulator

A simulator to genarate WSG data from refrence

Language: C++ - Size: 999 KB - Last synced at: 6 months ago - Pushed at: about 8 years ago - Stars: 4 - Forks: 0

jhayer/baargin

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

Language: Nextflow - Size: 15.4 MB - Last synced at: about 3 hours ago - Pushed at: 11 months ago - Stars: 7 - Forks: 0

GooglingTheCancerGenome/sv-gen

Snakemake-based workflow for generating artificial genomes with structural variants

Language: Python - Size: 22.5 MB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 7 - Forks: 1

annarchive/wgs2sgf

qq围棋wgs棋谱转sgf格式

Language: C++ - Size: 1.02 MB - Last synced at: about 2 months ago - Pushed at: almost 12 years ago - Stars: 9 - Forks: 6

galantelab/sideRETRO

A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Language: C - Size: 4.76 MB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 9 - Forks: 5

CoreArray/PySeqArray

PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)

Language: C++ - Size: 1.28 MB - Last synced at: 13 days ago - Pushed at: about 8 years ago - Stars: 14 - Forks: 0

senzhaocode/FuSViz_docs

Documentation of FuSViz app

Size: 28.6 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

dinesh2k19/amr

In this repository, we have compiled the WGS analysis schematics of the bacterial isolates obtained from poultry manure of layer and broiler poultry farms

Size: 1.78 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

suraiyajabin/ESKAPEE_pathogen

This repository saves Train/Test datasets used for training of ESKAPEE classification work and classification results publicly available at: https://www.techrxiv.org/doi/full/10.36227/techrxiv.21675053.v5

Size: 23.2 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

cvn001/transflow

A snakemake workflow for WGS-based tuberculosis transmission analysis

Language: HTML - Size: 249 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 14 - Forks: 6

Paleogenomics/IBDGem

Program for positive genetic identification and IBD detection from low-coverage sequencing data

Language: C - Size: 4.12 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

smail-lab-cmh/ga4k-sv-finder

Long read structural variants in rare disease cohort

Language: Python - Size: 47.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

CERC-Genomic-Medicine/WEGS_pipelines

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

Language: Nextflow - Size: 4.07 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

complexgenome/CUMC_taub

Language: R - Size: 374 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

FreekManders/Denovo_SNV_Analysis

De novo SNV analysis pipeline

Language: R - Size: 236 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 1

ToolsVanBox/SNVFI Fork of UMCUGenetics/SNVFI

Single Nucleotide Variant Filtering

Language: Shell - Size: 31.3 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

Kingsford-Group/kourami

Kourami: Graph-guided assembly for HLA alleles

Language: Java - Size: 19.2 MB - Last synced at: 11 months ago - Pushed at: over 6 years ago - Stars: 35 - Forks: 12

YogiOnBioinformatics/Joint-Genotyping-2021-2022

Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data

Language: Jupyter Notebook - Size: 646 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

kalilamali/Whole_genome_sequencing_analysis

Whole genome sequencing (WGS) was combined with bioinformatics tools to investigate the epidemiology of Vibrio cholerae in the Philippines and in other cholera affected countries.

Size: 7.37 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

rasigadelab/thd

Time-scaled haplotypic density (THD) implementation for R. Estimates epidemic success from pathogen genetic data.

Language: R - Size: 518 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

ruizhideng/wgs_pipeline

Language: Shell - Size: 5.72 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

TNTurnerLab/WTC-11

WTC-11 Genome Cell Line Analysis

Size: 19.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

richstoner/genomes

My personal genome in various forms from 23andMe and other WGS providers

Size: 4.81 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 1

auroramaurizio/my_DNA_seq_pipelines

In this repository I backup the pipelines I write for the project I am involved

Language: Python - Size: 2.85 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

zhukovanadezhda/schizophrenia-prediction

Language: Jupyter Notebook - Size: 1.27 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

mansikath/whole-genome-sequencing-pipeline

A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.

Language: HTML - Size: 1.96 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

AlexanderKononov/NGS-emulator

Detail WGS data simulation

Language: Python - Size: 2.54 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

AlexanderKononov/pipeline_cloneHD

Toolbox for work with CloneHD application

Language: Shell - Size: 13.7 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

FNL-MoCha/nextgenseq_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Language: Python - Size: 52.7 MB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 18 - Forks: 7

abukhalil-mohamed/geltowgs

Supplementary materials for the article entitled: Novel Algorithms for PFGE Bacterial Typing: Number of Co-Migrated DNA Fragments, Linking PFGE to WGS Results and Computer simulations for Evaluation of PulseNet International Typing Protocols

Size: 5.05 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

MatveySprindzuk/GenomicsSoftware

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

Size: 2.85 MB - Last synced at: almost 2 years ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

zhouzilu/iCNV

Integrated copy number variation detection toolset

Language: R - Size: 19.9 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 24 - Forks: 3

jimmlucas/DIvergenceTimes

Determination Of Divergence Times between sub populations. Used Data of WGS for prepare all the workflow.

Language: Shell - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sunnyosun/variantCalling

Variant calling of WGS datasets

Language: Shell - Size: 3.91 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

jfnavarro/hla_pipeline

DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions

Language: Python - Size: 1.55 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 2

songtaogui/pan-Zea_construct

Workflow to construct linear representation of pan genome from deep WGS data and public assemblies

Language: Shell - Size: 785 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 21 - Forks: 5

zhanghao-njmu/NGSmodule

A flexible, automation and pragmatic workflow tool to process the NGS data.

Language: R - Size: 1.98 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2

nmdp-bioinformatics/MiHAIP

Language: Java - Size: 16.7 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 3

jlanga/ttin_snps

Language: Python - Size: 35.5 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 2

KCCG/seave

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.

Language: HTML - Size: 21 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 15 - Forks: 3