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The Top 23 Variants Genomics Open Source Projects

Open source projects categorized as Variants Genomics
Categories > Science > Genomics
Categories > Variants
Deepvariant ⭐ 2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 5 months ago
Vg ⭐ 1,022
tools for working with genome variation graphs
most recent commit 3 months ago
Adam ⭐ 966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 3 months ago
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 6 months ago
Maftools ⭐ 400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
most recent commit 3 months ago
Vcfanno ⭐ 334
annotate a VCF with other VCFs/BEDs/tabixed files
dependent packages 1total releases 41most recent commit 5 months ago
Sarek ⭐ 299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 3 months ago
Octopus ⭐ 285
Bayesian haplotype-based mutation calling
most recent commit 8 months ago
Hap.py ⭐ 283
Haplotype VCF comparison tools
most recent commit 2 years ago
Rtg Tools ⭐ 260
RTG Tools: Utilities for accurate VCF comparison and manipulation
most recent commit 3 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16most recent commit 5 months ago
Slivar ⭐ 221
genetic variant expressions, annotation, and filtering for great good.
most recent commit 5 months ago
Ga4gh Schemas ⭐ 213
Models and APIs for Genomic data. RETIRED 2018-01-24
total releases 13most recent commit a year ago
Exomiser ⭐ 174
A Tool to Annotate and Prioritize Exome Variants
most recent commit 3 months ago
Smoove ⭐ 173
structural variant calling and genotyping with existing tools, but, smoothly.
total releases 23most recent commit 2 years ago
Souporcell ⭐ 134
Clustering scRNAseq by genotypes
most recent commit 6 months ago
Readthedocs ⭐ 133
Documentation for the Google Genomics cookbook.
most recent commit 4 years ago
Assemblytics ⭐ 124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
most recent commit 3 months ago
Benchmarking Tools ⭐ 110
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
most recent commit 4 years ago
Open Cravat ⭐ 98
A modular annotation tool for genomic variants
most recent commit 6 months ago
Ga4gh Server ⭐ 95
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
total releases 18most recent commit 6 years ago
Fermikit ⭐ 91
De novo assembly based variant calling pipeline for Illumina short reads
most recent commit 3 years ago
The 8 Most Depended On Variants Genomics Open Source Projects
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16latest release December 08, 2023most recent commit 5 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Genomicsdb ⭐ 88
High performance data storage for importing, querying and transforming variants.
dependent packages 2total releases 35latest release October 12, 2023most recent commit 3 months ago
Svtyper ⭐ 78
Bayesian genotyper for structural variants
dependent packages 1total releases 4latest release September 04, 2019most recent commit 4 years agopypi svtyper} Downloads
Vcfanno ⭐ 334
annotate a VCF with other VCFs/BEDs/tabixed files
dependent packages 1total releases 41latest release November 29, 2022most recent commit 5 months ago
Pandas Genomics ⭐ 42
Pandas ExtensionDtypes for dealing with genomics data
dependent packages 1total releases 21latest release July 01, 2022most recent commit a year agopypi pandas-genomics} Downloads
The 10 Latest Releases In Variants Genomics Open Source Projects
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16latest release December 08, 2023most recent commit 5 months ago
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Variantkey Nim ⭐ 5
nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
latest release November 27, 2023most recent commit 5 years ago
Dysgu ⭐ 75
Toolkit for calling structural variants using short or long reads
total releases 27latest release October 18, 2023most recent commit 6 months ago
Genomicsdb ⭐ 88
High performance data storage for importing, querying and transforming variants.
dependent packages 2total releases 35latest release October 12, 2023most recent commit 3 months ago
Vcfanno ⭐ 334
annotate a VCF with other VCFs/BEDs/tabixed files
dependent packages 1total releases 41latest release November 29, 2022most recent commit 5 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Cmdbtools ⭐ 21
Command line tools for CMDB varaints browser
total releases 14latest release July 06, 2022most recent commit 2 years ago
Pandas Genomics ⭐ 42
Pandas ExtensionDtypes for dealing with genomics data
dependent packages 1total releases 21latest release July 01, 2022most recent commit a year agopypi pandas-genomics} Downloads
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