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The Top 23 Genomics Variant Calling Open Source Projects

Open source projects categorized as Genomics Variant Calling
Categories > Science > Genomics
Categories > Variant Calling
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97most recent commit 4 months agopypi jcvi} Downloads
Vcflib ⭐ 591
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
most recent commit a month ago
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 6 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
Clair3 ⭐ 191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
most recent commit 3 months ago
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
most recent commit 4 years ago
Fermikit ⭐ 91
De novo assembly based variant calling pipeline for Illumina short reads
most recent commit 3 years ago
Genomicsdb ⭐ 88
High performance data storage for importing, querying and transforming variants.
dependent packages 2total releases 35most recent commit 3 months ago
Mccortex ⭐ 86
De novo genome assembly and multisample variant calling
most recent commit 5 years ago
Tiledb Vcf ⭐ 79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
most recent commit 3 months ago
Callings Nf ⭐ 76
GATK RNA-Seq Variant Calling in Nextflow
most recent commit 3 years ago
Dysgu ⭐ 75
Toolkit for calling structural variants using short or long reads
total releases 27most recent commit 6 months ago
Hla ⭐ 57
xHLA: Fast and accurate HLA typing from short read sequence data
most recent commit 6 years ago
Vcfdist ⭐ 48
vcfdist: Accurately benchmarking phased variant calls
most recent commit 3 months ago
Kevlar ⭐ 42
Reference-free variant discovery in large eukaryotic genomes
total releases 13most recent commit 3 years ago
Balsamic ⭐ 40
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
most recent commit 3 months ago
Indelope ⭐ 39
find large indels (in the blind spot between GATK/freebayes and SV callers)
most recent commit 6 years ago
Variantworks ⭐ 38
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
total releases 174most recent commit 2 years ago
Chm Eval ⭐ 37
most recent commit 4 years ago
Cerebra ⭐ 26
A tool for fast and accurate summarizing of variant calling format (VCF) files
total releases 15most recent commit 4 years ago
Arcsv ⭐ 19
Complex structural variant detection from WGS data
most recent commit 7 months ago
Clairs To ⭐ 18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
most recent commit 3 months ago
The 2 Most Depended On Genomics Variant Calling Open Source Projects
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
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months agopypi jcvi} Downloads
The 8 Latest Releases In Genomics Variant Calling Open Source Projects
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
Tbpore ⭐ 9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
total releases 11latest release October 11, 2023most recent commit 6 months ago
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months agopypi jcvi} Downloads
Snipgenie ⭐ 6
command line and desktop tool for microbial variant calling
total releases 2latest release November 01, 2021most recent commit 4 months ago
Cerebra ⭐ 26
A tool for fast and accurate summarizing of variant calling format (VCF) files
total releases 15latest release September 16, 2020most recent commit 4 years ago
Kevlar ⭐ 42
Reference-free variant discovery in large eukaryotic genomes
total releases 13latest release February 13, 2019most recent commit 3 years ago
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