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

Viral genomics analysis pipelines

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

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

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

A genome browser that shows long reads and complex variants better

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

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

A Suite of Packages for Analysis of Big Genomic Data

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

tools for working with genome variation graphs

Simulate genealogical trees and genomic sequence data using population genetic models

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

Intuitive local web frontend for the BLAST bioinformatics tool

Tools to process and analyze deep sequencing data.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Python library to handle Gene Ontology (GO) terms

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

The next version of bwa-mem

AQUAS TF and histone ChIP-seq pipeline

A modern genome browser built with JavaScript and HTML5.

Deep learning infrastructure for bioinformatics

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

Bioinformatics library for .NET

Efficient pythonic random access to fasta subsequences

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

An open source platform for managing and analyzing biomedical big data

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

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

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

annotate a VCF with other VCFs/BEDs/tabixed files

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

Fast genome-wide functional annotation through orthology assignment

Bayesian haplotype-based mutation calling

Example client programs for Saphetor's VarSome annotation API

Bayesian genotyper for structural variants

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Reads simulator

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

An interactive web tool for quality control of DNA sequencing data

BACNET is a Java based platform to develop website for multi-omics analysis

MISO: An open-source LIMS for NGS sequencing centres

A fast 23andMe genome text file parser, now superseded by arv

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

Predict plasmids from uncorrected long read data

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

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

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

Find causal cell-types underlying complex trait genetics

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

An ontology of cell types

Development repository for the Bioconductor package 'mixOmics '

A curated list of awesome bioinformatics software.

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

Framework for building fast genomics web tools with WebAssembly and WebWorkers

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

Analysis pipelines for sequencing data