1020 Open source projects that are alternatives of or similar to GenomicDataCommons

Bioconductor package for management of multi-assay data

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

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Compute N50/NG50 and auN/auNG

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

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

Reads simulator

Rapid large-scale prokaryote pan genome analysis

GenomeTools genome analysis system.

A powerful open source data warehouse system

JavaScript VisualizationTools

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

A cool place to store your Hi-C

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

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

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

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

A genome browser that shows long reads and complex variants better

nim wrapper for htslib for parsing genomics data files

Bystro genetic analysis (annotation, filtering, statistics)

cython + htslib == fast VCF and BCF processing

Haplotype VCF comparison tools

A package for designing compact and comprehensive capture probe sets.

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

An open-access bioinformatics text

Interactive R package to quantify, analyse and visualise alternative splicing

A collection of scripts and notes related to genomics and bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

NGLess: NGS with less work

Antimicrobial Resistance Identification By Assembly

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

A tool to circularize genome assemblies

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

GCP Essentials for Bioinformatics Researchers

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Bayesian haplotype-based mutation calling

Deep learning infrastructure for bioinformatics

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.

Bioinformatics library for .NET

An ultrafast memory-efficient short read aligner

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

Official git repository for Biopython (originally converted from CVS)

🔬 BEDOPS: high-performance genomic feature operations

Toolkit for preparing genomes for submission to NCBI

An interactive web portal for exploring immuno-oncology data

TCGA data acquisition and processing for Project Cognoma

A faster lmm for GWAS. Supports GPU backend.

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

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

Fast hash function for DNA sequences

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

Genomics Extension for SQLite

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

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