888 Open source projects that are alternatives of or similar to Jvarkit

Data intensive science for everyone.

Official code repository for GATK versions 4 and up

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

A package for designing compact and comprehensive capture probe sets.

NGLess: NGS with less work

UGENE is free open-source cross-platform bioinformatics software

A collection of scripts and notes related to genomics and bioinformatics

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

Curated (meta)list of resources for Biology.

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

An open-access bioinformatics text

A modern genome browser built with JavaScript and HTML5.

Tools to process and analyze deep sequencing data.

Ten Quick Tips for Deep Learning in Biology

Scripts to download genomes from the NCBI FTP servers

A powerful open source data warehouse system

Collection of scripts for bacterial genomics

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

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

This library tackles the construction and efficient execution of computational chemistry workflows

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

A faster lmm for GWAS. Supports GPU backend.

Toolkit for preparing genomes for submission to NCBI

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

annotate a VCF with other VCFs/BEDs/tabixed files

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

A library of free open source icons for science illustrations in biology and chemistry

A high-performance, Pythonic language for bioinformatics

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

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

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

Fast hash function for DNA sequences

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

Predict AMPs in (meta)genomes and peptides

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

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

🐳 Bio-dockers: dockerized bioinformatic tools

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

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

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

Compute N50/NG50 and auN/auNG

A comprehensive tutorial about GWAS and PRS

DOM Text Based Multiple Sequence Alignment Library

Feature Annotation Location Description Ontology

A simplified pipeline for ctDNA sequencing data analysis

Bystro genetic analysis (annotation, filtering, statistics)

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

An open source platform for managing and analyzing biomedical big data

Assembling the cause of phenotypes and genotypes from NGS data

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

An analysis and visualization platform for 'omics data

Method to optimally select samples for validation and resequencing

Provide R access to the NCI Genomic Data Commons portal.

Fast alignment and preprocessing of chromatin profiles

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.

Project metadata manager for PEPs in Python