cython + htslib == fast VCF and BCF processing
☆440Feb 23, 2026Updated 2 months ago
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☆401Aug 30, 2025Updated 8 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆149Feb 17, 2026Updated 2 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆847Apr 24, 2026Updated last week
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 7 months ago
- A Python package for exploring and analysing genetic variation data☆315Apr 1, 2026Updated last month
- 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.
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆313Apr 24, 2026Updated last week
- 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.☆107Dec 14, 2020Updated 5 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- Structural variant toolkit for VCFs☆407Mar 21, 2026Updated last month
- Haplotype VCF comparison tools☆465Dec 7, 2023Updated 2 years ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 2 months 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…☆889Apr 28, 2026Updated last week
- nim wrapper for htslib for parsing genomics data files☆158Updated this week
- 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.
- The D4 Quantitative Data Format☆172Nov 28, 2025Updated 5 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆676Mar 20, 2026Updated last month
- genetic variant expressions, annotation, and filtering for great good.☆272Updated this week
- Efficient pythonic random access to fasta subsequences☆485Mar 19, 2026Updated last month
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆133Oct 14, 2025Updated 6 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆144Aug 24, 2025Updated 8 months ago
- Cloud-native genomic dataframes and batch computing☆1,056Updated this week
- Population-scale genotyping using pangenome graphs☆197Jan 9, 2025Updated last year
- Performant Pythonic GenomicRanges☆495Apr 23, 2026Updated last week
- 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.
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 10 months ago
- a lightweight db framework for exploring genetic variation.☆327Apr 28, 2020Updated 6 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆109Jun 6, 2021Updated 4 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆183Apr 12, 2024Updated 2 years ago
- Scalable genetics toolkit☆275Mar 2, 2026Updated 2 months ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 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 2 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.☆365Jan 29, 2026Updated 3 months ago
- Python 3 library with good support for both reading and writing VCF☆112Oct 2, 2025Updated 7 months ago
- A tool set for short variant discovery in genetic sequence data.☆205May 4, 2021Updated 5 years ago
- tools for working with genome variation graphs☆1,307Updated 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☆149Updated this week