410 Open source projects that are alternatives of or similar to GenomicsDB

cython + htslib == fast VCF and BCF processing

Bioinformatics library for .NET

Deep learning infrastructure for bioinformatics

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

NGLess: NGS with less work

A comprehensive tutorial about GWAS and PRS

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

Reads simulator

Bayesian genotyper for structural variants

An ultrafast memory-efficient short read aligner

An interactive web tool for quality control of DNA sequencing data

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

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

Seven Bridges Genomics aligner/caller debugging and analysis tools

A collaboratively written review paper on deep learning, genomics, and precision medicine

Viral genomics analysis pipelines

Development repository for the Bioconductor package 'mixOmics '

Performant Pythonic GenomicRanges

Framework for building fast genomics web tools with WebAssembly and WebWorkers

structural variant calling and genotyping with existing tools, but, smoothly.

Guided synteny alignment between duplicated genomes (within specified quota constraint)

A WGS de novo assembler based on the FMD-index for large genomes

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

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

RADseq Data Exploration, Manipulation and Visualization using R

🔬 BEDOPS: high-performance genomic feature operations

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

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

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

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

Bayesian haplotype-based mutation calling

A Suite of Packages for Analysis of Big Genomic Data

Fast large scale matrix visualization for the web.

tools for working with genome variation graphs

MISO: An open-source LIMS for NGS sequencing centres

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

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

Tools to process and analyze deep sequencing data.

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

Python library to handle Gene Ontology (GO) terms

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

The next version of bwa-mem

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

A modern genome browser built with JavaScript and HTML5.

This repository collects the materials from the course "Foundations of HPC", 2021, at the Data Science and Scientific Computing Department, University of Trieste

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

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

Efficient pythonic random access to fasta subsequences

Intuitive local web frontend for the BLAST bioinformatics tool

An open source platform for managing and analyzing biomedical big data

An R package for creating Q-Q and manhattan plots from GWAS results

A high-performance, Pythonic language for bioinformatics

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

JavaScript VisualizationTools

A powerful open source data warehouse system

A cool place to store your Hi-C

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

annotate a VCF with other VCFs/BEDs/tabixed files

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