599 Open source projects that are alternatives of or similar to Hap.py

Spark VCF data source implementation for Dataframes

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

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

An ultrafast memory-efficient short read aligner

simple viewer for variant call format using htslib

Compute N50/NG50 and auN/auNG

A package for designing compact and comprehensive capture probe sets.

A curated list of bioinformatics bench-marking papers and resources.

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

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

JavaScript VisualizationTools

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Bayesian haplotype-based mutation calling

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

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

Assembling the cause of phenotypes and genotypes from NGS data

Home of the Genomic Feature and Variation Ontology (GFVO)

A curated list of awesome bioinformatics software.

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

Provide R access to the NCI Genomic Data Commons portal.

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.

De novo assembly based variant calling pipeline for Illumina short reads

Example client programs for Saphetor's VarSome annotation API

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

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

Official git repository for Biopython (originally converted from CVS)

Reads simulator

An interactive web tool for quality control of DNA sequencing data

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

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

A comprehensive tutorial about GWAS and PRS

An open source platform for managing and analyzing biomedical big data

Rapid large-scale prokaryote pan genome analysis

A high-performance, Pythonic language for bioinformatics

A fast and sensitive gapped read aligner

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

Python library to facilitate genome assembly, annotation, and comparative genomics

A cool place to store your Hi-C

Tools to process and analyze deep sequencing data.

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

highly-efficient & lightweight mutation signature matrix aggregation

Bioinformatics library for .NET

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

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

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

Analysis pipelines for sequencing data

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

Official code repository for GATK versions 4 and up

Genomics Extension for SQLite

GCP Essentials for Bioinformatics Researchers

A fast whole-genome aligner based on de Bruijn graphs

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Structural variant toolkit for VCFs

Antimicrobial Resistance Identification By Assembly

Inference of ploidy and heterozygosity structure using whole genome sequencing data

BioGrakn Knowledge Graph

Viral genomics analysis pipelines

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.