569 Open source projects that are alternatives of or similar to Minigraph

A powerful open source data warehouse system

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

A genome browser that shows long reads and complex variants better

Ten Quick Tips for Deep Learning in Biology

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

Scalable genomic data analysis.

GenomeTools genome analysis system.

Analysis pipelines for sequencing data

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

Antimicrobial Resistance Identification By Assembly

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

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

The next version of bwa-mem

Reads simulator

Tools to process and analyze deep sequencing data.

Rapid large-scale prokaryote pan genome analysis

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

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

A fast whole-genome aligner based on de Bruijn graphs

Bayesian genotyper for structural variants

nim wrapper for htslib for parsing genomics data files

Genomics Extension for SQLite

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

A tool to circularize genome assemblies

A modern genome browser built with JavaScript and HTML5.

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

A fast and sensitive gapped read aligner

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

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

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

Scripts to download genomes from the NCBI FTP servers

Data intensive science for everyone.

Java utilities for Bioinformatics

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Official code repository for GATK versions 4 and up

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

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

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

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

Efficient pythonic random access to fasta subsequences

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

An interactive web tool for quality control of DNA sequencing data

Bayesian haplotype-based mutation calling

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

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

NGLess: NGS with less work

A cool place to store your Hi-C

Deep learning infrastructure for bioinformatics

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

An open source platform for managing and analyzing biomedical big data

A comprehensive tutorial about GWAS and PRS

Model and predict short DNA sequence features with neural networks

A collection of scripts and notes related to genomics and bioinformatics

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

Intuitive local web frontend for the BLAST bioinformatics tool