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

Collection of scripts for bacterial genomics

PERF is an Exhaustive Repeat Finder

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

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

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

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

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

Compute N50/NG50 and auN/auNG

Bystro genetic analysis (annotation, filtering, statistics)

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

Assembling the cause of phenotypes and genotypes from NGS data

Haplotype VCF comparison tools

nim wrapper for htslib for parsing genomics data files

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

Bayesian haplotype-based mutation calling

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

Example client programs for Saphetor's VarSome annotation API

Earl Grey: A fully automated TE curation and annotation pipeline

An open source platform for managing and analyzing biomedical big data

A fast 23andMe genome text file parser, now superseded by arv

Java utilities for Bioinformatics

Efficient pythonic random access to fasta subsequences

Reinforced Recommendation toolkit built around pytorch 1.7

A comprehensive tutorial about GWAS and PRS

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

A modern genome browser built with JavaScript and HTML5.

Tools to process and analyze deep sequencing data.

JavaScript VisualizationTools

Data intensive science for everyone.

Scalable genomic data analysis.

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

Curated list of framework component libraries for UI styles/toolkit

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

Small Broadcast Receiver Library for Android

Genomic Data Retrieval with R

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

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

A fast whole-genome aligner based on de Bruijn graphs

Model and predict short DNA sequence features with neural networks

Genomics Extension for SQLite

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

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

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

Next generation sequencing reads de novo assembler.

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

NGLess: NGS with less work

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

A cool place to store your Hi-C

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.

Genome annotation with AUGUSTUS

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

A modular-designed and easy-to-use microservices framework in Go.

Core BioPerl 1.x code

Official git repository for Biopython (originally converted from CVS)

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

A collection of scripts and notes related to genomics and bioinformatics

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