569 Open source projects that are alternatives of or similar to Wgsim

A React web application to query and share any PostgreSQL database.

The next version of bwa-mem

Scalable genomic data analysis.

A collection of scripts and notes related to genomics and bioinformatics

An open source platform for managing and analyzing biomedical big data

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Ten Quick Tips for Deep Learning in Biology

Antimicrobial Resistance Identification By Assembly

Python library to facilitate genome assembly, annotation, and comparative genomics

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

GCP Essentials for Bioinformatics Researchers

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

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

Genomics Extension for SQLite

cython + htslib == fast VCF and BCF processing

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

A faster lmm for GWAS. Supports GPU backend.

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

An ultrafast memory-efficient short read aligner

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Fast hash function for DNA sequences

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Simple pure Python SAM parser and objects for working with SAM records

Provide R access to the NCI Genomic Data Commons portal.

An open-access bioinformatics text

Rapid large-scale prokaryote pan genome analysis

An interactive web tool for quality control of DNA sequencing data

A fast 23andMe genome text file parser, now superseded by arv

Predict plasmids from uncorrected long read data

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

A curated list of awesome bioinformatics software.

Bayesian genotyper for structural variants

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

A modern genome browser built with JavaScript and HTML5.

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

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Model and predict short DNA sequence features with neural networks

A Practical and Efficient NCBI Taxonomy Toolkit

variant expressions, annotation, and filtering for great good.

SortMeRNA: next-generation sequence filtering and alignment tool

BioGrakn Knowledge Graph

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Simulate genealogical trees and genomic sequence data using population genetic models

A comprehensive library for computational molecular biology

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Viral genomics analysis pipelines

pymzML - an interface between Python and mzML Mass spectrometry Files

MISO: An open-source LIMS for NGS sequencing centres

Demonstrating best practices for bioinformatics command line tools

Next generation sequencing reads de novo assembler.

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

AQUAS TF and histone ChIP-seq pipeline

✏️ A versatile DNA sequence optimizer