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

A collection of scripts and notes related to genomics and bioinformatics

Bayesian genotyper for structural variants

annotate a VCF with other VCFs/BEDs/tabixed files

Scalable genomic data analysis.

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

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

cython + htslib == fast VCF and BCF processing

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

JavaScript VisualizationTools

GenomeTools genome analysis system.

Deep learning infrastructure for bioinformatics

A powerful open source data warehouse system

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

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

An interactive web tool for quality control of DNA sequencing data

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

Toolset for SV simulation, comparison and filtering

A fast whole-genome aligner based on de Bruijn graphs

🔬 BEDOPS: high-performance genomic feature operations

Reads simulator

Rapid large-scale prokaryote pan genome analysis

Antimicrobial Resistance Identification By Assembly

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

NGLess: NGS with less work

Intuitive local web frontend for the BLAST bioinformatics tool

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

An ultrafast memory-efficient short read aligner

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

Analysis pipelines for sequencing data

Official code repository for GATK versions 4 and up

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

A tool to circularize genome assemblies

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

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

A genome browser that shows long reads and complex variants better

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

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

Model and predict short DNA sequence features with neural networks

Official git repository for Biopython (originally converted from CVS)

Ten Quick Tips for Deep Learning in Biology

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Genomics Extension for SQLite

A cool place to store your Hi-C

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

Structural variant toolkit for VCFs

nim wrapper for htslib for parsing genomics data files

Bayesian haplotype-based mutation calling

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Syntax highlighting for computational biology

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

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

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

Data intensive science for everyone.

highly-efficient & lightweight mutation signature matrix aggregation

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