GitHub topics: variant-analysis
gmboowa/mtb-mixed-infection-pipeline
mtb-mixed-infection-pipeline enables detection of mixed Mycobacterium tuberculosis infections using a reproducible workflow that integrates Snippy, FreeBayes (pooled mode) & MixInfect2. It processes raw reads through alignment, variant calling & statistical analysis to identify mixed-strain infections
Language: R - Size: 1.46 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
IBCHgenomic/genovaranno
Variant annotation human genomics
Language: Rust - Size: 344 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0
IBCHgenomic/vcfilter
population scale variant filter
Language: Rust - Size: 70.3 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0
IBCHgenomic/rustcivic
rust json client for civic database
Language: Rust - Size: 1.19 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0
mansikath/Variant-calling
Repository for variant calling utilizing bioinformatics tools and databases
Size: 10.7 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0
biocommons/anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
Language: Python - Size: 745 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 13 - Forks: 5
biocommons/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Language: Python - Size: 21.9 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 269 - Forks: 96
fullscreen-triangle/gospel
Python framework for comprehensive variant detection in whole genome sequences using advanced machine learning models for cross domain pattern recognition in fitness, pharmacogenetics and nutritional aspects of sprint running
Language: Python - Size: 4.39 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
KarchinLab/open-cravat
A modular annotation tool for genomic variants
Language: JavaScript - Size: 9.25 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 121 - Forks: 33
zhengzhenxian/Repun
An accurate small variant representation unification method for multiple sequencing platforms
Language: Python - Size: 180 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 1
Zilong-Li/vcfpp
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
Language: C++ - Size: 1.89 MB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 22 - Forks: 4
AppThreat/atom
atom is a novel intermediate representation for applications and a standalone tool that is powered by chen.
Language: Rust - Size: 18.6 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 65 - Forks: 3
KalinNonchev/gnomAD_DB
This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.
Language: Python - Size: 17.7 MB - Last synced at: 6 days ago - Pushed at: 14 days ago - Stars: 45 - Forks: 10
IBCHgenomic/webanno
a unified platform for variant search
Language: TypeScript - Size: 31.3 KB - Last synced at: 16 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0
RWilton/Arioc
Arioc: GPU-accelerated DNA short-read alignment
Size: 16.9 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 69 - Forks: 9
Integrative-Transcriptomics/MUSIAL
Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.
Language: Java - Size: 291 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 5 - Forks: 1
Paulanerus/TextExplorer
A tool designed for the exploration, analysis, and comparison of textual data variants.
Language: Kotlin - Size: 543 KB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 3 - Forks: 0
jonas-fuchs/virHEAT
Visualize microbial evolution at the SNP level!
Language: Python - Size: 736 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 14 - Forks: 6
Illumina/PlatinumGenomes
The Platinum Genomes Truthset
Size: 8.79 KB - Last synced at: 6 days ago - Pushed at: over 7 years ago - Stars: 88 - Forks: 9
IBCHgenomic/eVaiutilities
eVaiutilities for eVaianalyzer-human genomics
Language: Rust - Size: 84.1 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0
bigbio/hvantk
Hail variant annotation toolkit
Language: Python - Size: 20.3 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0
bio-ontology-research-group/EmbedPVP
EmbedPVP: Embedding-based Phenotype Variant Predictor
Language: Python - Size: 176 KB - Last synced at: 23 days ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 0
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
Language: Rust - Size: 214 KB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 153 - Forks: 10
jajik123/GenAnalyzer
GenAnalyzer is a web application designed for the analysis of protein sequences, mutation detection, and exploring their links to genetic diseases. Built using Flask, this tool integrates data from UniProt and ClinVar for efficient bioinformatics analysis.
Language: JavaScript - Size: 2.03 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
biocommons/biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
Language: Python - Size: 523 KB - Last synced at: 28 days ago - Pushed at: about 2 months ago - Stars: 41 - Forks: 35
oicr-gsi/variantMerging
a workflow for combining variant calls from SNV analyses done with different callers
Language: Python - Size: 595 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
LeoooJR/VCFDelta
VCFDelta
Language: Python - Size: 456 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
EUCANCan/variant-extractor
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
Language: Python - Size: 6.5 MB - Last synced at: about 21 hours ago - Pushed at: 3 months ago - Stars: 7 - Forks: 1
NagaComBio/TiNDA
Tumor in normal detection
Language: R - Size: 1.23 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1
githubsatelliteworkshops/codeql
GitHub Satellite 2020 workshops on finding security vulnerabilities with CodeQL for Java/JavaScript.
Size: 2.93 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 210 - Forks: 47
patois/HexraysToolbox
Hexrays Toolbox - Find code patterns within the Hexrays ctree
Language: Python - Size: 247 KB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 455 - Forks: 44
biocoderdev/weap
WEAP: An automatic and accelerated pipeline for analysing multi-sample whole exome sequencing data
Language: Shell - Size: 2.64 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
biocommons/seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
Language: Python - Size: 310 KB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 5
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
Language: Nim - Size: 3.25 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 255 - Forks: 23
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
Language: C# - Size: 110 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 32 - Forks: 1
madsondeluna/getvar_mvp
O GetVar é útil para o auxílio a diagnósticos genéticos e aconselhamentos, permitindo decisões baseadas em dados com respaldo científico, otimizando tempo e servindo de suporte ao sistema de decisão clínico.
Language: HTML - Size: 350 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
biocommons/bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
Language: Python - Size: 1.67 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 22 - Forks: 18
madsondeluna/getvar_containerized
O GetVar é útil para o auxílio a diagnósticos genéticos e aconselhamentos, permitindo decisões baseadas em dados com respaldo científico, otimizando tempo e servindo de suporte ao sistema de decisão clínico.
Language: HTML - Size: 330 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - 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: about 2 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
tsnorri/vcf2multialign
Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.
Language: C++ - Size: 1.2 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 1
bihealth/auto-acmg
Automatic classification of sequence variants and CNVs according to ACMG criteria.
Language: Python - Size: 42.6 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 7 - Forks: 0
quadram-institute-bioscience/tatajuba
Identification and classification of homopolymeric tracts from reads.
Language: C - Size: 177 MB - Last synced at: 6 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 0
dbmi-bgm/granite Fork of bgm-cwg/novoCaller
A collection of software to work with genomic variants
Language: Python - Size: 46 MB - Last synced at: 22 days ago - Pushed at: 9 months ago - Stars: 6 - Forks: 0
clbenoit/SomaVarDB
R Shiny app for somatic genomic variants interpretation. The tool suite to deal with the underlying local structured database is provided here : https://github.com/clbenoit/SomaVarDBTools
Language: R - Size: 36.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
clbenoit/GermlineVarDB
R Shiny app for germline genomic variants interpretation. The tool suite to deal with the underlying local structured database is provided here : https://github.com/clbenoit/GermlineVarDBTools
Language: R - Size: 36.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
yjx1217/simuG
simuG: a general-purpose genome simulator
Language: Perl - Size: 5.17 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 83 - Forks: 11
biocommons/biocommons.github.io
biocommons website
Language: Python - Size: 3.19 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 2
LOVDnl/LOVDplus
LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.
Language: PHP - Size: 25.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1
tin-z/coccinelle_exercises
coccinelle notes and exercises
Language: SmPL - Size: 10.7 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0
biocommons/.github
Organization-wide GitHub configuration
Size: 34.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
NCBI-Hackathons/ApeShape
A Prototype for Defining the Ancestral Alleles for Ones that Modify Human Phenotypes
Language: Python - Size: 518 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 2
Illumina/happyCompare 📦
Reporting toolbox for happy output
Language: R - Size: 105 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 4
Illumina/happyR
R tools to interact with hap.py output
Language: R - Size: 60 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 15 - Forks: 1
biocommons/actions
GitHub Actions used by biocommons repos
Size: 6.84 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
cccnrc/plot-VCF
visual analysis of your VCF files
Language: R - Size: 75.9 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 2
NeuroSyd/ngs-variant-analysis
Novel mutations are identified in leukemia through variant analysis.
Size: 1.25 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
mklarqvist/tachyon
High-level API for storing and querying sequence variant data
Language: C++ - Size: 8.03 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 20 - Forks: 3
Yandell-Lab/VVP-pub
VVP (VAAST Variant Prioritizer) rapidly prioritizes genetic variants
Language: C - Size: 1.08 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 19 - Forks: 13
parvathisudha/Targeted-Panel-Analysis
Targeted Panel Analysis pipeline
Language: Shell - Size: 44.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1
Derick80/variant_alleles
A PoC in using ACMG guidelines to classify variants
Language: TypeScript - Size: 8.38 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
KenSaville/Variant-Caller
A Latch Bio workflow to call DNA sequence variants
Language: Python - Size: 6.84 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
EstherOlabisi/Bioinformatics-work
Several bioinformatics projects: sequence alignment, machine learning, GUI development, etc.
Language: R - Size: 13.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
bio-ontology-research-group/phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
Language: Java - Size: 6.53 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 34 - Forks: 13
jhuapl-bio/AGAVE
Automated Genomics Application for Variant Exploration (AGAVE)
Language: Vue - Size: 15.7 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
krishb2x/VCFStats
to analyze multiple VCF files and generate a summary of variant metrics
Language: Python - Size: 11.7 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0
adamd3/VarPredict
A command line tool for predicting gene expression using genotypic data
Language: Python - Size: 2.15 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
Tammimies-Lab/circRNA_neuro
Manuscript data and code repository
Size: 21.5 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
nickzren/atav-database
A relational database stores per sample based sequencing data.
Language: Python - Size: 18.7 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1
nickzren/atav
A comprehensive platform for population-scale genomic analyses
Language: Java - Size: 181 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 3
a-thind/IBDVar
A tool for prioritising identity-by-descent (IBD) variants in Whole Genome Sequencing (WGS) data from families with rare heritable diseases.
Language: Shell - Size: 4.79 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
mtekman/ngs_sequencing_pipeline 📦
Skeleton for NGS pipeline, now backbone of OVAS project
Language: Python - Size: 296 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
bioinfonupeb/molecular-markers-on-sports
Identification of molecular markers for sports performance
Language: HTML - Size: 4.75 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
ucdavis-bioinformatics-training/2017-August-Variant-Analysis-Workshop
From SNP and structural variant calling to GWAS.
Language: HTML - Size: 67.1 MB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 6 - Forks: 5
elowy01/vcf_filtering
Filter a VCF to discard false positive variants
Language: Python - Size: 72.3 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0
chinmayaNK22/Variant-Proteome-DB-Generator
A python command line based script for extraction of annotated variants from VCF file, generating variant proteome database and to check the uniqueness of variant proteins from the database search.
Language: Python - Size: 3.03 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
NCBI-Hackathons/ClinVar_in_3D
Mapping Clinically Relevant Mutations to Protein Structures
Language: HTML - Size: 148 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 6
fei0810/Triti-Map
A Snakemake-based pipeline for gene mapping in Triticeae.
Language: Python - Size: 200 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 1
NCBI-Hackathons/chromatinonlinedatabase
An Online Database of 3D Chromatin Structure
Language: PHP - Size: 17.2 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 2
NCBI-Hackathons/Complex_Phenogeno
Mapping complex genotypes to phenotypic subclusters
Language: Python - Size: 93.8 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 5 - Forks: 0
sung/ObsGynaePipes
Bioinformatics pipelines developed while working at the dept of Obs & Gynae
Language: R - Size: 32.2 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
shiltemann/Virtual-Normal-Correction
Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full
Language: Shell - Size: 18.7 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 3
sfilges/umiAnalyzer
Tools for analyzing UMIErrorCorrect output
Language: R - Size: 18.3 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2
ALAPY/AGx
Variant annotation and filtration server ALAPY Genome Explorer
Language: Shell - Size: 1020 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 3 - Forks: 0
odb9402/KS-Evol Fork of pko89403/Monte-Carlo_Based_KS-Test
KS-Evol : Non-parametric hypothesis testing for time-series genomic variants using Monte Carlo based Komogrov-Smirnov test
Language: C - Size: 128 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
quinlan-lab/mendacity
language-agnostic testing for inheritance models
Language: Python - Size: 7.81 KB - Last synced at: 6 days ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 2
tsnorri/vcfdistances
Calculate SMD and Hamming and Jaccard distances between each pair of samples in a set of variant files.
Language: C++ - Size: 45.9 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
wm75/mimodd-lib
a core part of the MiModD package for use as a library
Language: Python - Size: 37.1 KB - Last synced at: 2 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
knkarthik/biotoolbelt
A collection of web tools for biologists
Language: Python - Size: 39.1 KB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1
