1278 Open source projects that are alternatives of or similar to Genomics

simple viewer for variant call format using htslib

tools for reading, writing, merging, and remapping SNPs

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

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

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

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

A faster lmm for GWAS. Supports GPU backend.

Method to optimally select samples for validation and resequencing

A fast whole-genome aligner based on de Bruijn graphs

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Finds SNP sites from a multi-FASTA alignment file

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Bystro genetic analysis (annotation, filtering, statistics)

Compute N50/NG50 and auN/auNG

An open-access bioinformatics text

Provide R access to the NCI Genomic Data Commons portal.

Fast and flexible ORF finder

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

Fast alignment and preprocessing of chromatin profiles

Home of the Genomic Feature and Variation Ontology (GFVO)

A library to build and execute typed scientific workflows

Genotyping of segregating mobile elements insertions

Predict plasmids from uncorrected long read data

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

De novo assembly based variant calling pipeline for Illumina short reads

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

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.

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

Earl Grey: A fully automated TE curation and annotation pipeline

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

Robust and efficient workflows using a simple language agnostic approach

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

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

A high-performance, Pythonic language for bioinformatics

An analysis and visualization platform for 'omics data

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

A comprehensive tutorial about GWAS and PRS

Plant image analysis using OpenCV

Signal-level algorithms for MinION data

The next version of bwa-mem

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

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Tools to process and analyze deep sequencing data.

A modern genome browser built with JavaScript and HTML5.

Workflow Description Language - Specification and Implementations

Scripts to download genomes from the NCBI FTP servers

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Example client programs for Saphetor's VarSome annotation API

A fast and sensitive gapped read aligner

C library for high-throughput sequencing data formats

tools for working with genome variation graphs

Generic germline variant annotation pipeline

🌈Scaffold genome sequence assemblies using linked read sequencing data

DEPRECIATED! Please use nf-core/tools instead

A versatile pairwise aligner for genomic and spliced nucleotide sequences