cython + htslib == fast VCF and BCF processing
☆450Sep 10, 2026Updated last month
Alternatives and similar repositories for cyvcf2
Users that are interested in cyvcf2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- annotate a VCF with other VCFs/BEDs/tabixed files☆403Jun 16, 2026Updated 3 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆152Feb 17, 2026Updated 7 months ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆227Sep 18, 2025Updated last year
- a lightweight db framework for exploring genetic variation.☆328Apr 28, 2020Updated 6 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆878May 2, 2026Updated 5 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A Python package for exploring and analysing genetic variation data☆318Oct 1, 2026Updated last week
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆339Sep 30, 2026Updated 2 weeks ago
- Plot structural variant signals from many BAMs and CRAMs☆574Jul 13, 2024Updated 2 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆109Dec 14, 2020Updated 5 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆266Jun 17, 2024Updated 2 years ago
- Structural variant toolkit for VCFs☆424Oct 3, 2026Updated last week
- Bayesian haplotype-based mutation calling☆327Feb 13, 2026Updated 8 months ago
- Haplotype VCF comparison tools☆474Dec 7, 2023Updated 2 years ago
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆912Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- The D4 Quantitative Data Format☆176Nov 28, 2025Updated 10 months ago
- python access to UCSC genomes database☆138Aug 27, 2020Updated 6 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆686Oct 2, 2026Updated last week
- genetic variant expressions, annotation, and filtering for great good.☆274May 12, 2026Updated 5 months ago
- pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)☆49Mar 3, 2017Updated 9 years ago
- Interval data structure☆235Mar 18, 2026Updated 6 months ago
- nim wrapper for htslib for parsing genomics data files☆159Sep 30, 2026Updated 2 weeks ago
- Efficient pythonic random access to fasta subsequences☆490Sep 3, 2026Updated last month
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆132Oct 14, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Cloud-native genomic dataframes and batch computing☆1,080Updated this week
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆146Aug 24, 2025Updated last year
- Population-scale genotyping using pangenome graphs☆202Jan 9, 2025Updated last year
- Performant Pythonic GenomicRanges☆491Sep 23, 2026Updated 3 weeks ago
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆120Jun 6, 2021Updated 5 years ago
- Scalable genetics toolkit☆285Sep 21, 2026Updated 3 weeks ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 2 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆346Feb 22, 2026Updated 7 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆51Apr 9, 2021Updated 5 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆190Apr 12, 2024Updated 2 years ago
- tools for working with genome variation graphs☆1,343Updated this week
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆330Aug 26, 2026Updated last month
- ☆36Aug 13, 2020Updated 6 years ago
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.☆374Aug 17, 2026Updated last month