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Top 185 genomics open source projects

Hap.py
Haplotype VCF comparison tools
Cyvcf2
cython + htslib == fast VCF and BCF processing
Dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Bowtie
An ultrafast memory-efficient short read aligner
Htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
Pyranges
Performant Pythonic GenomicRanges
Miniasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Bedops
🔬 BEDOPS: high-performance genomic feature operations
Genomeworks
SDK for GPU accelerated genome assembly and analysis
Higlass
Fast large scale matrix visualization for the web.
Flowcraft
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Minigraph
Proof-of-concept seq-to-graph mapper and graph generator
Juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Sequenceserver
Intuitive local web frontend for the BLAST bioinformatics tool
Deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Ribbon
A genome browser that shows long reads and complex variants better
Ideogram
Chromosome visualization for the web
Janggu
Deep learning infrastructure for bioinformatics
Wgsim
Reads simulator
Roary
Rapid large-scale prokaryote pan genome analysis
Goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Glow
An open-source toolkit for large-scale genomic analysis
Viral Ngs
Viral genomics analysis pipelines
Vcfr
Tools to work with variant call format files
Smoove
structural variant calling and genotyping with existing tools, but, smoothly.
✭ 147
gogenomics
Biomartr
Genomic Data Retrieval with R
Awesome Bioinformatics Benchmarks
A curated list of bioinformatics bench-marking papers and resources.
Hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Artemis
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
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Octopus
Bayesian haplotype-based mutation calling
Hts Nim
nim wrapper for htslib for parsing genomics data files
Miso Lims
MISO: An open-source LIMS for NGS sequencing centres
Benchmarking Tools
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Kmer Cnt
Code examples of fast and simple k-mer counters for tutorial purposes
Circlator
A tool to circularize genome assemblies
Hicexplorer
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Ngless
NGLess: NGS with less work
Qqman
An R package for creating Q-Q and manhattan plots from GWAS results
Cooler
A cool place to store your Hi-C
Cgranges
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Slivar
variant expressions, annotation, and filtering for great good.
✭ 110
nimgenomics
Msprime
Simulate genealogical trees and genomic sequence data using population genetic models
Genomics
A collection of scripts and notes related to genomics and bioinformatics
Smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Ariba
Antimicrobial Resistance Identification By Assembly
Chipseq pipeline
AQUAS TF and histone ChIP-seq pipeline
Gcp For Bioinformatics
GCP Essentials for Bioinformatics Researchers
Bio
Bioinformatics library for .NET
Dkm
Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features
Igv Snapshot Automator
Script to automatically create and run IGV snapshot batchscripts
Awesome 10x Genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
1-60 of 185 genomics projects