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The Top 23 Variants Variant Calling Open Source Projects

Open source projects categorized as Variants Variant Calling
Categories > Variant Calling
Categories > Variants
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
Pepper ⭐ 216
PEPPER-Margin-DeepVariant
total releases 8most recent commit 6 months ago
Megalodon ⭐ 172
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
dependent packages 1total releases 24most recent commit a year agopypi megalodon} Downloads
Vt ⭐ 163
A tool set for short variant discovery in genetic sequence data.
most recent commit 3 years ago
Clairvoyante ⭐ 142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
most recent commit 3 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
Clair ⭐ 74
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
most recent commit 3 years ago
Hla ⭐ 57
xHLA: Fast and accurate HLA typing from short read sequence data
most recent commit 6 years ago
Bayestyper ⭐ 52
A method for variant graph genotyping based on exact alignment of k-mers
most recent commit 5 years ago
Ococo ⭐ 39
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
most recent commit 5 years ago
Chm Eval ⭐ 37
most recent commit 4 years ago
Indigo ⭐ 29
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
most recent commit 6 months ago
Cerebra ⭐ 26
A tool for fast and accurate summarizing of variant calling format (VCF) files
total releases 15most recent commit 4 years ago
Varca ⭐ 20
Use an ensemble of variant callers to call variants from ATAC-seq data
most recent commit 2 years ago
Clairs To ⭐ 18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
most recent commit 3 months ago
Vipr ⭐ 10
Assembly and intrahost / low-frequency variant calling for viral samples
most recent commit 4 years ago
The 2 Most Depended On Variants Variant Calling Open Source Projects
The 5 Latest Releases In Variants 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
Pepper ⭐ 216
PEPPER-Margin-DeepVariant
total releases 8latest release November 19, 2020most recent commit 6 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
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