324 Open source projects that are alternatives of or similar to wgd

Simulate genealogical trees and genomic sequence data using population genetic models

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

AQUAS TF and histone ChIP-seq pipeline

Configuration tutorials for a variety of mail user agents.

Bioinformatics library for .NET

A genome browser that shows long reads and complex variants better

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

JavaScript VisualizationTools

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

Deep learning infrastructure for bioinformatics

Bayesian genotyper for structural variants

Find target sites for the miRNAs in genomic sequences

An interactive web tool for quality control of DNA sequencing data

Reads simulator

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

cython + htslib == fast VCF and BCF processing

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

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

Development repository for the Bioconductor package 'mixOmics '

A Framework for Coalescent Simulation in R

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Viral genomics analysis pipelines

An ultrafast memory-efficient short read aligner

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

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

RADseq Data Exploration, Manipulation and Visualization using R

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

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

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

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

Performant Pythonic GenomicRanges

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

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

A Suite of Packages for Analysis of Big Genomic Data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

tools for working with genome variation graphs

Bayesian haplotype-based mutation calling

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

🔬 BEDOPS: high-performance genomic feature operations

Tools to process and analyze deep sequencing data.

MISO: An open-source LIMS for NGS sequencing centres

Python library to handle Gene Ontology (GO) terms

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

The next version of bwa-mem

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

A modern genome browser built with JavaScript and HTML5.

Fast large scale matrix visualization for the web.

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

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

Efficient pythonic random access to fasta subsequences

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

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

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

Population assignment analysis using R

Genomics Workflows on AWS

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

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

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