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

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Sentieon DNAseq

De novo assembly based variant calling pipeline for Illumina short reads

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

A tool for fast and accurate summarizing of variant calling format (VCF) files

xHLA: Fast and accurate HLA typing from short read sequence data

find large indels (in the blind spot between GATK/freebayes and SV callers)

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Complex structural variant detection from WGS data

De novo genome assembly and multisample variant calling

Ten Quick Tips for Deep Learning in Biology

Chromosome visualization for the web

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

This repository provides easy automation scripts for building a HPC environment in Azure. It also includes examples to build e2e environment and run some of the key HPC benchmarks and applications.

Rapid large-scale prokaryote pan genome analysis

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

An open-source toolkit for large-scale genomic analysis

Tools to work with variant call format files

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

Genomic Data Retrieval with R

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

API Specififications

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

SDK for GPU accelerated genome assembly and analysis

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

nim wrapper for htslib for parsing genomics data files

A genome browser that shows long reads and complex variants better

cython + htslib == fast VCF and BCF processing

Deep learning infrastructure for bioinformatics

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Reads simulator

An ultrafast memory-efficient short read aligner

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

Seven Bridges Genomics aligner/caller debugging and analysis tools

Viral genomics analysis pipelines

Performant Pythonic GenomicRanges

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

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

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

🔬 BEDOPS: high-performance genomic feature operations

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

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

Bayesian haplotype-based mutation calling

Fast large scale matrix visualization for the web.

MISO: An open-source LIMS for NGS sequencing centres

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

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

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

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

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

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

Haplotype VCF comparison tools

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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.

Intuitive local web frontend for the BLAST bioinformatics tool

NGLess: NGS with less work

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

JavaScript VisualizationTools