273 Open source projects that are alternatives of or similar to Higlass

A collection of scripts and notes related to genomics and bioinformatics

Script to automatically create and run IGV snapshot batchscripts

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A cool place to store your Hi-C

A friendly next-generation interface for Genomic data discovery powered by InterMine

Genomic Data Retrieval with R

GCP Essentials for Bioinformatics Researchers

Ten Quick Tips for Deep Learning in Biology

A fast whole-genome aligner based on de Bruijn graphs

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

NGLess: NGS with less work

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Tools to work with variant call format files

variant expressions, annotation, and filtering for great good.

Chromosome visualization for the web

Antimicrobial Resistance Identification By Assembly

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

Genomics Extension for SQLite

A powerful open source data warehouse system

Pan-genome wide association studies

nim wrapper for htslib for parsing genomics data files

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

Rapid large-scale prokaryote pan genome analysis

Model and predict short DNA sequence features with neural networks

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

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

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Viral genomics analysis pipelines

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

A genome browser that shows long reads and complex variants better

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

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

Simulate genealogical trees and genomic sequence data using population genetic models

Intuitive local web frontend for the BLAST bioinformatics tool

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

AQUAS TF and histone ChIP-seq pipeline

Deep learning infrastructure for bioinformatics

Bioinformatics library for .NET

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

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

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

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

Bayesian haplotype-based mutation calling

Bayesian genotyper for structural variants

Reads simulator

An interactive web tool for quality control of DNA sequencing data

MISO: An open-source LIMS for NGS sequencing centres

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

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

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

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

Development repository for the Bioconductor package 'mixOmics '

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

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

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

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

GenomeTools genome analysis system.

An open-source toolkit for large-scale genomic analysis

A tool to circularize genome assemblies