600 Open source projects that are alternatives of or similar to Nucleus

A collection of scripts and notes related to genomics and bioinformatics

Data intensive science for everyone.

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

A curated list of awesome bioinformatics software.

A fast 23andMe genome text file parser, now superseded by arv

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Efficient pythonic random access to fasta subsequences

Official git repository for Biopython (originally converted from CVS)

Analysis pipelines for sequencing data

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

Numerical Encoding for Human Genetic Variants

Ultrafast sequence typing and gene detection from NGS raw reads

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

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

A simple command-line tool to download data from Joint Genome Institute databases

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

Toolkit for preparing genomes for submission to NCBI

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

Fast hash function for DNA sequences

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

Bystro genetic analysis (annotation, filtering, statistics)

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Compute N50/NG50 and auN/auNG

Fast and flexible ORF finder

The next version of bwa-mem

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

Haplotype VCF comparison tools

A package for designing activity-informed nucleic acid diagnostics for viruses.

JavaScript VisualizationTools

Java utilities for Bioinformatics

A faster lmm for GWAS. Supports GPU backend.

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

A modern genome browser built with JavaScript and HTML5.

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

A comprehensive tutorial about GWAS and PRS

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

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

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

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

An open source platform for managing and analyzing biomedical big data

cython + htslib == fast VCF and BCF processing

Tools to process and analyze deep sequencing data.

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

A high-performance, Pythonic language for bioinformatics

Assembling the cause of phenotypes and genotypes from NGS data

A fast and sensitive gapped read aligner

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

annotate a VCF with other VCFs/BEDs/tabixed files

Provide R access to the NCI Genomic Data Commons portal.

Fast alignment and preprocessing of chromatin profiles

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

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

Earl Grey: A fully automated TE curation and annotation pipeline

De novo assembly based variant calling pipeline for Illumina short reads

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

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.

Example client programs for Saphetor's VarSome annotation API

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

Ultrafast de novo assembly for long noisy reads (though having no consensus step)