cython + htslib == fast VCF and BCF processing
☆445May 14, 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☆407May 1, 2026Updated last month
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆150Feb 17, 2026Updated 3 months ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆227Sep 18, 2025Updated 8 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆858May 2, 2026Updated last month
- A Python package for exploring and analysing genetic variation data☆316Jun 1, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆320Apr 24, 2026Updated last month
- Plot structural variant signals from many BAMs and CRAMs☆567Jul 13, 2024Updated last year
- don't get DUP'ed or DEL'ed by your putative SVs.☆108Dec 14, 2020Updated 5 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆266Jun 17, 2024Updated last year
- Structural variant toolkit for VCFs☆414May 22, 2026Updated 3 weeks ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 4 months ago
- Haplotype VCF comparison tools☆469Dec 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…☆894Jun 3, 2026Updated last week
- nim wrapper for htslib for parsing genomics data files☆158May 2, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- The D4 Quantitative Data Format☆172Nov 28, 2025Updated 6 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆680Mar 20, 2026Updated 2 months ago
- genetic variant expressions, annotation, and filtering for great good.☆275May 12, 2026Updated last month
- Efficient pythonic random access to fasta subsequences☆486Mar 19, 2026Updated 2 months ago
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆133Oct 14, 2025Updated 8 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆144Aug 24, 2025Updated 9 months ago
- Cloud-native genomic dataframes and batch computing☆1,064Updated this week
- Population-scale genotyping using pangenome graphs☆199Jan 9, 2025Updated last year
- Performant Pythonic GenomicRanges☆495Apr 23, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- a lightweight db framework for exploring genetic variation.☆329Apr 28, 2020Updated 6 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆109Jun 6, 2021Updated 5 years ago
- Scalable genetics toolkit☆277Mar 2, 2026Updated 3 months ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 2 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆185Apr 12, 2024Updated 2 years ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆51Apr 9, 2021Updated 5 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆342Feb 22, 2026Updated 3 months ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆330Mar 16, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.☆366Jan 29, 2026Updated 4 months ago
- Python 3 library with good support for both reading and writing VCF☆112Oct 2, 2025Updated 8 months ago
- A tool set for short variant discovery in genetic sequence data.☆206May 4, 2021Updated 5 years ago
- tools for working with genome variation graphs☆1,322Updated this week
- create a gemini-compatible database from a VCF☆55Jan 5, 2021Updated 5 years ago
- a pileup library that embraces the huge☆43Oct 2, 2020Updated 5 years ago
- Per-base per-nucleotide depth analysis☆149May 9, 2026Updated last month