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

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

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

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

A simple command-line tool to download data from Joint Genome Institute databases

find large indels (in the blind spot between GATK/freebayes and SV callers)

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

JavaScript VisualizationTools

Deep learning infrastructure for bioinformatics

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Toolkit for preparing genomes for submission to NCBI

nim wrapper for htslib for parsing genomics data files

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Compute N50/NG50 and auN/auNG

Official git repository for Biopython (originally converted from CVS)

An open-access bioinformatics text

Bystro genetic analysis (annotation, filtering, statistics)

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

Method to optimally select samples for validation and resequencing

Rapid large-scale prokaryote pan genome analysis

Fast alignment and preprocessing of chromatin profiles

Genotyping of segregating mobile elements insertions

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Code examples of fast and simple k-mer counters for tutorial purposes

Predict plasmids from uncorrected long read data

A tool to circularize genome assemblies

Home of the Genomic Feature and Variation Ontology (GFVO)

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

BACNET is a Java based platform to develop website for multi-omics analysis

NGLess: NGS with less work

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A high-performance, Pythonic language for bioinformatics

A comprehensive tutorial about GWAS and PRS

A React web application to query and share any PostgreSQL database.

A fast and sensitive gapped read aligner

Ultra-fast and memory-efficient (meta-)genome assembler

Intuitive local web frontend for the BLAST bioinformatics tool

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

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

C library for high-throughput sequencing data formats

The next version of bwa-mem

Data intensive science for everyone.

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

Structural variant toolkit for VCFs

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Bioinformatics library for .NET

Official code repository for GATK versions 4 and up

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

Antimicrobial Resistance Identification By Assembly

Model and predict short DNA sequence features with neural networks

An interactive web tool for quality control of DNA sequencing data

Example client programs for Saphetor's VarSome annotation API

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

A fast whole-genome aligner based on de Bruijn graphs

Genomics Extension for SQLite

GCP Essentials for Bioinformatics Researchers

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Package for fetching metadata and downloading data from SRA/ENA/GEO

Genomic Data Retrieval with R