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Search results for genome vcf
genome
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vcf
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106 search results found
Vg
⭐
1,022
tools for working with genome variation graphs
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Nanopolish
⭐
496
Signal-level algorithms for MinION data
Samplot
⭐
458
Plot structural variant signals from many BAMs and CRAMs
Vcftools
⭐
415
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Hap.py
⭐
283
Haplotype VCF comparison tools
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Pcgr
⭐
234
Personal Cancer Genome Reporter (PCGR)
Gridss
⭐
212
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Lancet
⭐
145
Microassembly based somatic variant caller for NGS data
Sigprofilerextractor
⭐
132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Variantspark
⭐
121
machine learning for genomic variants
Vcf Kit
⭐
107
VCF-kit: Assorted utilities for the variant call format
Peddy
⭐
104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Pandora
⭐
98
Pan-genome inference and genotyping with long noisy or short accurate reads
Genomewarp
⭐
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
⭐
87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Parliament2
⭐
83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Mocha
⭐
70
MOsaic CHromosomal Alterations (MoChA) caller
Bcbio.variation
⭐
66
Toolkit to analyze genomic variation data, built on the GATK with Clojure
Simug
⭐
58
simuG: a general-purpose genome simulator
Snpsplit
⭐
43
Allele-specific alignment sorting
Platinumgenomes
⭐
42
The Platinum Genomes Truthset
Broad Prod Wgs Germline Snps Indels
⭐
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
Indelope
⭐
39
find large indels (in the blind spot between GATK/freebayes and SV callers)
Gtctovcf
⭐
39
Script to convert GTC/BPM files to VCF
Novograph
⭐
36
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
Gwasvcf
⭐
36
Reading, querying and writing GWAS summary data in VCF format
Genomeuplot
⭐
32
The Genome U-Plot is a JavaScript tool to visualize chromosomal abnormalities in the Human Genome using a U-shape layout.
Popdel
⭐
32
Population-wide Deletion Calling
Circleator
⭐
32
Flexible circular visualization of genome-associated data with BioPerl and SVG.
Introgression Detection
⭐
31
Mutserve
⭐
29
mtDNA Variant Caller
Gwasglue
⭐
28
Linking GWAS data to analytical tools in R
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Gsort
⭐
26
sort genomic data
Gwaspipeline
⭐
26
Cgppindel
⭐
25
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Vcf2fasta
⭐
25
Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file
1000_genomes_examples
⭐
23
Examples using R and 1000 genomes data
Gssplayground
⭐
21
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
Proxysnps
⭐
21
🔖 Get SNP proxies from the 1000 Genomes Project.
Genome Server 21
⭐
20
Serve your genotypes and phenotypes via an API for satoshis
Checkvcf
⭐
20
Sanity check Variant Call Format (VCF) files.
Rnaseq Nf
⭐
20
RNAseq analysis pipeline
Helmsman
⭐
19
highly-efficient & lightweight mutation signature matrix aggregation
Ekidna
⭐
19
Assembly based core genome SNP alignments for bacteria
Workshop Popgenome
⭐
19
Tutorial about R package PopGenome
Pynnotator
⭐
19
This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.
Smurf
⭐
19
Samchain
⭐
18
Ivc
⭐
17
Integrated Variant Caller
Svcollector
⭐
17
Method to optimally select samples for validation and resequencing
Snp_notes
⭐
17
Notes on SNP-related tools and genome variation analysis
Sigprofilermatrixgeneratorr
⭐
17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Vargeno
⭐
15
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Sgdp Fermi
⭐
15
FermiKit small variant calls for public SGDP samples
Anno
⭐
15
Anno is a variant annotation tool
Vcf2pop
⭐
15
Phenopredict21
⭐
15
Command line tool to predict phenotype from VCF (gets models from pheno-server-21)
Rmap
⭐
15
Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS
Parsecnv2
⭐
14
Parse Copy Number Variation from Array and Sequencing
Snapperdb
⭐
14
Varifier
⭐
13
Variant call verification
Hadoopcnv
⭐
12
HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data
Rpga
⭐
12
Typete
⭐
12
Genotyping of segregating mobile elements insertions
Bcfanno
⭐
12
A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file
Acmg Penetrance
⭐
11
Penetrance estimates; frequency and distribution of secondary findings for the ACMG-59 gene panel
Deepsv
⭐
11
Calling deletions using deep convolutional neural
Forge
⭐
11
Code for building and testing variant ranking strategies
Sigprofilerextractorr
⭐
11
An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Wtchg Rg
⭐
10
Reliable Genome project
Cau Tibetanwheatseq
⭐
10
Customized codes used in Tibetan wheat sequencing project.
Lira
⭐
10
Snpmatch
⭐
9
A simple python library to identify the most likely strain from the population
Psite
⭐
9
Simulate next-generation sequencing reads for tumor samples
Gsalign
⭐
9
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
Toil Vg
⭐
9
Distributed and cloud computing framework for vg
Psmcr
⭐
9
R Port of psmc
Gatk For Microbes
⭐
8
Varmatch
⭐
8
robust matching of small variant datasets using flexible scoring schemes
Pseudoref
⭐
8
Make Pseudo-Reference Genome from VCF/BCF
Wes.wgs
⭐
7
Covid-19 HGI WES/WGS burden test BQC-19 pipeline
Varcomp
⭐
7
Tools for calling and comparing variants from simulated read sets
Ipat
⭐
7
iPat allows you to perform GWAS and GS with drags and clicks!
Lift Over Vcf
⭐
7
UCSC liftOver (genome build converter) for vcf format
Genome
⭐
7
🔬 Beau Gunderson's genetic data
Sim1000g
⭐
7
Simulation of rare and common variants based on 1000 genomes data
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Popgen
⭐
6
A collection of scripts I wrote when doing population genetics: calculate GC content, perform the McDonald-Kreitman test, calculate Tajima's D, convert VCF files to FASTA files using a reference genome
Tomatula
⭐
6
Afplot
⭐
6
Plot allele frequencies in VCF files
Presm
⭐
6
Personalized Reference Editor for Somatic Mutation discovery in cancer genomics
Asdpex
⭐
6
Precisionmedicinetoolkit
⭐
6
Search public databases for given genotypic information
Vcf2diploid
⭐
6
personal genome constructor
Aselux
⭐
6
Related Searches
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Variants Vcf (406)
C Plus Plus Genome (400)
1-100 of 106 search results
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