1142 Open source projects that are alternatives of or similar to Hail

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

annotate a VCF with other VCFs/BEDs/tabixed files

Bayesian genotyper for structural variants

A collection of scripts and notes related to genomics and bioinformatics

cython + htslib == fast VCF and BCF processing

Official code repository for GATK versions 4 and up

Haplotype VCF comparison tools

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

A faster lmm for GWAS. Supports GPU backend.

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

Fast hash function for DNA sequences

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

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

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Method to optimally select samples for validation and resequencing

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

An open-access bioinformatics text

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

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

Provide R access to the NCI Genomic Data Commons portal.

Fast alignment and preprocessing of chromatin profiles

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

Earl Grey: A fully automated TE curation and annotation pipeline

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

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Spark VCF data source implementation for Dataframes

simple viewer for variant call format using htslib

Scripts to download genomes from the NCBI FTP servers

A DNA Sequence Alignment/Map (SAM) library for Clojure

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

Toolkit for preparing genomes for submission to NCBI

Simple pure Python SAM parser and objects for working with SAM records

An open-source toolkit for large-scale genomic analysis

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Compute N50/NG50 and auN/auNG

Bystro genetic analysis (annotation, filtering, statistics)

A package for designing compact and comprehensive capture probe sets.

Tools to process and analyze deep sequencing data.

Assembling the cause of phenotypes and genotypes from NGS data

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A fast 23andMe genome text file parser, now superseded by arv

Predict plasmids from uncorrected long read data

De novo assembly based variant calling pipeline for Illumina short reads

Home of the Genomic Feature and Variation Ontology (GFVO)

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

Example client programs for Saphetor's VarSome annotation API

A curated list of awesome bioinformatics software.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

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

C library for high-throughput sequencing data formats

A comprehensive tutorial about GWAS and PRS

An open source platform for managing and analyzing biomedical big data

Efficient pythonic random access to fasta subsequences

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

A high-performance, Pythonic language for bioinformatics

Java utilities for Bioinformatics

A fast and sensitive gapped read aligner

Genotyping of segregating mobile elements insertions