2222 Open source projects that are alternatives of or similar to Genometools

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

annotate a VCF with other VCFs/BEDs/tabixed files

Official code repository for GATK versions 4 and up

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

🔬 BEDOPS: high-performance genomic feature operations

A package for designing compact and comprehensive capture probe sets.

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

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

A genome browser that shows long reads and complex variants better

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.

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

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

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

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

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

🌈Scaffold genome sequence assemblies using linked read sequencing data

Rapid large-scale prokaryote pan genome analysis

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

Genomics Extension for SQLite

An interactive web tool for quality control of DNA sequencing data

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Bioinformatics library for .NET

Data intensive science for everyone.

Scalable genomic data analysis.

Ten Quick Tips for Deep Learning in Biology

Curated list of framework component libraries for UI styles/toolkit

Reads simulator

Small Broadcast Receiver Library for Android

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

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

Model and predict short DNA sequence features with neural networks

A cool place to store your Hi-C

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

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

Analysis pipelines for sequencing data

Bayesian genotyper for structural variants

A fast whole-genome aligner based on de Bruijn graphs

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

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

A collection of scripts and notes related to genomics and bioinformatics

NGLess: NGS with less work

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

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

Genome annotation with AUGUSTUS

Antimicrobial Resistance Identification By Assembly

A tool to circularize genome assemblies

Build your own chat UI with React components in few minutes. Chat UI Kit from chatscope is an open source UI toolkit for developing web chat applications.

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Genomic Data Retrieval with R

Bayesian haplotype-based mutation calling

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