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Search results for variants genome
genome
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variants
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7 search results found
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Vg
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1,022
tools for working with genome variation graphs
Biotools
⭐
525
A list of useful bioinformatics resources
Samplot
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458
Plot structural variant signals from many BAMs and CRAMs
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Awesome Cancer Variant Databases
⭐
284
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Hap.py
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283
Haplotype VCF comparison tools
Gemini
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272
a lightweight db framework for exploring genetic variation.
Pcgr
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234
Personal Cancer Genome Reporter (PCGR)
Hgvs
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226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Pepper
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216
PEPPER-Margin-DeepVariant
Doc Annovar
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193
Documentation for the ANNOVAR software
Regenie
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148
regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
Lancet
⭐
145
Microassembly based somatic variant caller for NGS data
Dna Seq Analysis
⭐
128
DNA sequencing analysis notes from Ming Tang
Assemblytics
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124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Variantspark
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121
machine learning for genomic variants
Benchmarking Tools
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110
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Vcf Kit
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107
VCF-kit: Assorted utilities for the variant call format
Genomewarp
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96
GenomeWarp translates genetic variants from one genome assembly version to another.
Expecto
⭐
95
predicting expression effects of human genome variants ab initio from sequence
Pipeline Structural Variation
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87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Mccortex
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86
De novo genome assembly and multisample variant calling
Parliament2
⭐
83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Sv Cnv Studies
⭐
81
📚 Relevant papers for CNV and SV approaches
Svtools
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79
Tools for processing and analyzing structural variants.
Clair
⭐
74
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Mocha
⭐
70
MOsaic CHromosomal Alterations (MoChA) caller
Pisces
⭐
67
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
Bcbio.variation
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66
Toolkit to analyze genomic variation data, built on the GATK with Clojure
Variant Qc
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61
Quality control methods for human genomic variants.
Transcriptclean
⭐
57
Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
Clinsv
⭐
51
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
Cadd Scripts
⭐
50
CADD scripts release for offline scoring. For more information about CADD, please visit our website
Svim Asm
⭐
48
Structural Variant Identification Method using Genome Assemblies
Covizu
⭐
45
Rapid analysis and visualization of coronavirus genome variation
Bactmap
⭐
45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Mtoolbox
⭐
44
A bioinformatics pipeline to analyze mtDNA from NGS data
Svmu
⭐
42
A program to call variants from genome alignment
Platinumgenomes
⭐
42
The Platinum Genomes Truthset
Seqarray
⭐
41
Data management of large-scale whole-genome sequence variant calls (Development version only)
Broad Prod Wgs Germline Snps Indels
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39
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-geno
Gtctovcf
⭐
39
Script to convert GTC/BPM files to VCF
Lrsim
⭐
38
10x Genomics Reads Simulator
Isaac_variant_caller
⭐
38
This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka
Gean
⭐
36
This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species.
Discosnp
⭐
35
DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
Crossstitch
⭐
35
Code for phasing SVs with SNPs
Genome Data Integration
⭐
35
Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls
Variantspark
⭐
34
VariantSpark is a framework for applying Spark-based Machine Learning methods to whole-genome variant information
Grocsvs
⭐
32
Genome-wide reconstruction of complex structural variants
Mapcaller
⭐
32
MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
Dicey
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32
In-silico PCR, primer design and padlock design for in-situ sequencing
Mtbseq_source
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32
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
Introgression Detection
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31
Mindthegap
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30
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
Mutserve
⭐
29
mtDNA Variant Caller
Gotcloud
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29
Genomes on the Cloud, Mapping & Variant Calling Pipelines
Persvade
⭐
27
perSVade: personalized Structural Variation detection
Deepvariant
⭐
26
Deep Variant as a Nextflow pipeline
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
1000 Genomes Genetic Maps
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23
Genetic maps interpolated to sites in the 1000 Genomes project
Varnote
⭐
23
Fast and scalable variant annotation tool
1000_genomes_examples
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23
Examples using R and 1000 genomes data
Giab_tools_methods
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22
This repository contains a list of tools or methods that have been used in GIAB analysis
Seqmule
⭐
21
Automated human exome/genome variants detection from FASTQ files
Pipeline Umi Amplicon
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21
Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
Genomeanalysismodule
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21
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Primerdesign
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20
A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants
Clamms
⭐
20
CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
Checkvcf
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20
Sanity check Variant Call Format (VCF) files.
1000g Integration
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19
variant integration methods for the 1000 Genomes Project
Mageri
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19
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
Varapp Backend Py
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18
Django backend to varapp
Topmed_variant_calling
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18
Hugeseq
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18
For original Nature Biotechnology Publication (Q1 2012)
Svcollector
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17
Method to optimally select samples for validation and resequencing
Snp_notes
⭐
17
Notes on SNP-related tools and genome variation analysis
Ivc
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17
Integrated Variant Caller
Gatk4 Genome Processing Pipeline
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16
Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.
Rmats Dvr
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16
Anno
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15
Anno is a variant annotation tool
Crg2
⭐
15
Research pipeline for exploring clinically relevant genomic variants
Eagle
⭐
15
Hgvslib
⭐
15
hgvslib provides functions to parse and compare the equivalency of variant strings described according to Human Genome Variation Society (HGVS) syntax.
Sgdp Fermi
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15
FermiKit small variant calls for public SGDP samples
Bcbio_validation_workflows
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14
A community menagarie of automated variant validations using bcbio and the Common Workflow Language
Snapperdb
⭐
14
Structural_variant_comparison
⭐
14
SV
Driverml
⭐
14
Pwas
⭐
14
Proteome-Wide Association Study
Pavfinder
⭐
14
🔍 Post Assembly Variants Finder
Crispritz
⭐
14
Tool package to perform in-silico CRISPR analysis and assessment
Ngs_dna
⭐
13
NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC
Varifier
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13
Variant call verification
Falcon Genome
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13
Falcon Accelerated Genomics Pipelines
Lava
⭐
13
LAVA: Lightweight Assignment of Variant Alleles
Gnomad_python_api
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13
🧬 gnomAD Python API is used to obtain data from gnomAD (genome aggregation database).
Crisflash
⭐
13
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