599 Open source projects that are alternatives of or similar to Cyvcf2

Scalable genomic data analysis.

Bayesian genotyper for structural variants

A collection of scripts and notes related to genomics and bioinformatics

annotate a VCF with other VCFs/BEDs/tabixed files

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Haplotype VCF comparison tools

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Official code repository for GATK versions 4 and up

Ten Quick Tips for Deep Learning in Biology

An ultrafast memory-efficient short read aligner

A genome browser that shows long reads and complex variants better

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A collection of publications on comparison of high-throughput sequencing technologies.

Model and predict short DNA sequence features with neural networks

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Analysis pipelines for sequencing data

Proof-of-concept seq-to-graph mapper and graph generator

Flexible genotype query among 30,000+ samples whole-genome

A fast whole-genome aligner based on de Bruijn graphs

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A Java API for high-throughput sequencing data (HTS) formats.

Syntax highlighting for computational biology

A powerful open source data warehouse system

GenomeTools genome analysis system.

🔬 BEDOPS: high-performance genomic feature operations

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

NGLess: NGS with less work

A tool to circularize genome assemblies

highly-efficient & lightweight mutation signature matrix aggregation

Deep learning infrastructure for bioinformatics

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Toolset for SV simulation, comparison and filtering

Data intensive science for everyone.

Reads simulator

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Rapid large-scale prokaryote pan genome analysis

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

An interactive web tool for quality control of DNA sequencing data

Antimicrobial Resistance Identification By Assembly

GCP Essentials for Bioinformatics Researchers

Intuitive local web frontend for the BLAST bioinformatics tool

Bioinformatics library for .NET

A cool place to store your Hi-C

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Genomics Extension for SQLite

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

nim wrapper for htslib for parsing genomics data files

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Bayesian haplotype-based mutation calling

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

C library for high-throughput sequencing data formats

Python and C++ code for reading and writing genomics data.

Structural variant toolkit for VCFs