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Search results for bioinformatics vcf
bioinformatics
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vcf
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85 search results found
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Htslib
⭐
762
C library for high-throughput sequencing data formats
Nucleus
⭐
675
Python and C++ code for reading and writing genomics data.
Bioawk
⭐
518
BWK awk modified for biological data
Nanopolish
⭐
496
Signal-level algorithms for MinION data
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Cyvcf2
⭐
345
cython + htslib == fast VCF and BCF processing
Vcfanno
⭐
334
annotate a VCF with other VCFs/BEDs/tabixed files
Survivor
⭐
299
Toolset for SV simulation, comparison and filtering
Truvari
⭐
284
Structural variant toolkit for VCFs
Hap.py
⭐
283
Haplotype VCF comparison tools
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Somalier
⭐
224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Biosyntax
⭐
184
Syntax highlighting for computational biology
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Poplddecay
⭐
138
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
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.
Mutscan
⭐
127
Detect and visualize target mutations by scanning FastQ files directly
Variantspark
⭐
121
machine learning for genomic variants
Peddy
⭐
104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Cljam
⭐
87
A DNA Sequence Alignment/Map (SAM) library for Clojure
Snps
⭐
82
tools for reading, writing, merging, and remapping SNPs
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtyper
⭐
78
Bayesian genotyper for structural variants
Vcfpy
⭐
78
Python 3 library with good support for both reading and writing VCF
Bgt
⭐
76
Flexible genotype query among 30,000+ samples whole-genome
Hadoop Bam
⭐
66
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
Opengene.jl
⭐
61
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Transanno
⭐
54
accurate LiftOver tool for new genome assemblies
Jannovar
⭐
51
Annotation of VCF variants with functional impact and from databases (executable+library)
Sv2
⭐
50
Support Vector Structural Variation Genotyper
Vembrane
⭐
50
vembrane filters VCF records using python expressions
Vcfdist
⭐
48
vcfdist: Accurately benchmarking phased variant calls
Snpsplit
⭐
43
Allele-specific alignment sorting
Hts Nim Tools
⭐
41
useful command-line tools written to show-case hts-nim
Nphase
⭐
39
Ploidy agnostic phasing pipeline and algorithm
Fuc
⭐
38
Frequently used commands in bioinformatics
Gwas2vcf
⭐
37
Convert GWAS summary statistics to VCF
Gor
⭐
37
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
Popdel
⭐
32
Population-wide Deletion Calling
Biotoolbox
⭐
27
Tools for querying and analysis of genomic data
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
Cutevcf
⭐
23
simple viewer for variant call format using htslib
Iliad
⭐
21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
Proxysnps
⭐
21
🔖 Get SNP proxies from the 1000 Genomes Project.
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
Sv Pipeline
⭐
21
Pipeline for structural variation detection in cohorts
Cmdbtools
⭐
21
Command line tools for CMDB varaints browser
Common_analyses
⭐
20
Repository of common bioinformatics scripts
Helmsman
⭐
19
highly-efficient & lightweight mutation signature matrix aggregation
Sigprofilermatrixgeneratorr
⭐
17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Svcollector
⭐
17
Method to optimally select samples for validation and resequencing
Ontologies
⭐
16
Home of the Genomic Feature and Variation Ontology (GFVO)
Hmtnote
⭐
15
Human mitochondrial variants annotation using HmtVar.
Vargeno
⭐
15
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Rmap
⭐
15
Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS
Mitty
⭐
13
Seven Bridges Genomics aligner/caller debugging and analysis tools
Rsidx
⭐
12
Library for indexing VCF files for random access searches by rsID
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.
Divbrowse
⭐
10
A web application for interactive visualization and exploratory data analysis of variant call matrices
Hts Rdf
⭐
9
Managing sequencing data with RDF
High Perf Bio
⭐
9
Open-source toolkit that simplifies and speeds up work with bioinformatics data. high-perf-bio allows you easily upload VCF, BED or arbitrary tables to DB and execute popular bioinformatic queries without MongoDB Query Language knowledge.
Variantconvert
⭐
9
A customizable genetic variants file format converter.
Vcfpp
⭐
9
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
Gap2seq
⭐
9
Gap2Seq is a gap filling and insertion genotyping tool.
Pseudoref
⭐
8
Make Pseudo-Reference Genome from VCF/BCF
Variantcallformat.jl
⭐
8
Read and write VCF and BCF files
Agaat
⭐
7
Automated Tool for Global Screening Array analysis
Rbcf
⭐
7
R Bindings for htslib/bcf
Malva
⭐
7
genotyping by Mapping-free ALternate-allele detection of known VAriants
Popgen
⭐
7
Small scripts for population genetics analysis
Bamsplit
⭐
7
Split a BAM file by haplotype support
Bamscope
⭐
7
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Ebt
⭐
6
Evolutionary Bioinformatics Toolkit (EBT)
Unmasc
⭐
6
Tumor-only variant calling
Dhtslib
⭐
6
D bindings and OOP wrappers for htslib
Vcfppr
⭐
6
Rapid processing of VCF/BCF files in R!
Afplot
⭐
6
Plot allele frequencies in VCF files
Vizsnp St
⭐
5
Visualizing the effect of SNPs on protein structure using iCn3D
Varity
⭐
5
Variant translation library for Clojure
Clinical_variant_database
⭐
5
Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset. Originally developed as part of a Masters in Bioinformatics project @ University of Exeter
Vase
⭐
5
Variant Annotation, Segregation and Exclusion for family or cohort based rare-disease sequencing studies.
Recallme
⭐
5
Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer
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