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The Top 23 Genomics Vcf Open Source Projects

Open source projects categorized as Genomics Vcf
Categories > Science > Genomics
Categories > Science > Vcf
Vg ⭐ 1,022
tools for working with genome variation graphs
most recent commit 3 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146most recent commit 3 months agopypi hail} Downloads
Nucleus ⭐ 675
Python and C++ code for reading and writing genomics data.
dependent packages 2total releases 18most recent commit 3 years agopypi google-nucleus} Downloads
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 6 months ago
Cyvcf2 ⭐ 345
cython + htslib == fast VCF and BCF processing
dependent packages 46total releases 90most recent commit 3 months agopypi cyvcf2} Downloads
Vcfanno ⭐ 334
annotate a VCF with other VCFs/BEDs/tabixed files
dependent packages 1total releases 41most recent commit 5 months ago
Truvari ⭐ 284
Structural variant toolkit for VCFs
total releases 23most recent commit 16 days ago
Hap.py ⭐ 283
Haplotype VCF comparison tools
most recent commit 2 years ago
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78most recent commit 4 months ago
Rtg Tools ⭐ 260
RTG Tools: Utilities for accurate VCF comparison and manipulation
most recent commit 3 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16most recent commit 5 months ago
Somalier ⭐ 224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
most recent commit 7 months ago
Kipoi ⭐ 222
Kipoi's model zoo API
dependent packages 7total releases 73most recent commit 9 months agopypi kipoi} Downloads
Slivar ⭐ 221
genetic variant expressions, annotation, and filtering for great good.
most recent commit 5 months ago
Smoove ⭐ 173
structural variant calling and genotyping with existing tools, but, smoothly.
total releases 23most recent commit 2 years ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 years ago
Genozip ⭐ 144
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
total releases 132most recent commit 3 months ago
Jigv ⭐ 115
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
most recent commit 10 months ago
Peddy ⭐ 104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
most recent commit 3 years ago
Cljam ⭐ 87
A DNA Sequence Alignment/Map (SAM) library for Clojure
total releases 37most recent commit 3 months ago
Tiledb Vcf ⭐ 79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
most recent commit 3 months ago
Svtyper ⭐ 78
Bayesian genotyper for structural variants
dependent packages 1total releases 4most recent commit 4 years agopypi svtyper} Downloads
The 10 Most Depended On Genomics Vcf Open Source Projects
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago
Cyvcf2 ⭐ 345
cython + htslib == fast VCF and BCF processing
dependent packages 46total releases 90latest release December 11, 2023most recent commit 3 months agopypi cyvcf2} Downloads
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16latest release December 08, 2023most recent commit 5 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Kipoi ⭐ 222
Kipoi's model zoo API
dependent packages 7total releases 73latest release June 14, 2022most recent commit 9 months agopypi kipoi} Downloads
Disq ⭐ 31
A library for manipulating bioinformatics sequencing formats in Apache Spark
dependent packages 3total releases 10latest release February 09, 2021most recent commit 8 months ago
Nucleus ⭐ 675
Python and C++ code for reading and writing genomics data.
dependent packages 2total releases 18latest release August 31, 2021most recent commit 3 years agopypi google-nucleus} Downloads
Genotype ⭐ 7
Simple genotype comparison of VCF files
dependent packages 1total releases 9latest release September 23, 2020most recent commit a year agopypi genotype} 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
Svtyper ⭐ 78
Bayesian genotyper for structural variants
dependent packages 1total releases 4latest release September 04, 2019most recent commit 4 years agopypi svtyper} Downloads
The 10 Latest Releases In Genomics Vcf Open Source Projects
Cyvcf2 ⭐ 345
cython + htslib == fast VCF and BCF processing
dependent packages 46total releases 90latest release December 11, 2023most recent commit 3 months agopypi cyvcf2} Downloads
Vcfr ⭐ 225
Tools to work with variant call format files
dependent packages 29total releases 16latest release December 08, 2023most recent commit 5 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago
Truvari ⭐ 284
Structural variant toolkit for VCFs
total releases 23latest release August 07, 2023most recent commit 16 days 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
Cmdbtools ⭐ 21
Command line tools for CMDB varaints browser
total releases 14latest release July 06, 2022most recent commit 2 years ago
Kipoi ⭐ 222
Kipoi's model zoo API
dependent packages 7total releases 73latest release June 14, 2022most recent commit 9 months agopypi kipoi} Downloads
Vcf2fhir ⭐ 20
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
total releases 9latest release May 26, 2022most recent commit 2 years ago
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