936 Open source projects that are alternatives of or similar to Deepvariant

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

A collection of scripts and notes related to genomics and bioinformatics

UGENE is free open-source cross-platform bioinformatics software

NGLess: NGS with less work

A Java API for high-throughput sequencing data (HTS) formats.

Analysis pipelines for sequencing data

Java utilities for Bioinformatics

Collection of scripts for bacterial genomics

GenomeTools genome analysis system.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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

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.

Efficient pythonic random access to fasta subsequences

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

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

An interactive web tool for quality control of DNA sequencing data

Official git repository for Biopython (originally converted from CVS)

Rapid large-scale prokaryote pan genome analysis

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

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

Genomics Extension for SQLite

🌈Scaffold genome sequence assemblies using linked read sequencing data

Antimicrobial Resistance Identification By Assembly

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Assembling the cause of phenotypes and genotypes from NGS data

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A curated list of awesome bioinformatics software.

A tool to circularize genome assemblies

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

A fast 23andMe genome text file parser, now superseded by arv

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

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

A genome browser that shows long reads and complex variants better

🔬 Assemble large genomes using short reads

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

Ultrafast sequence typing and gene detection from NGS raw reads

A repository for setting up a RNAseq workflow

Tools to process and analyze deep sequencing data.

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

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

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

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

Tools for working with genomic and high throughput sequencing data.

ABRA2

Model and predict short DNA sequence features with neural networks

Ten Quick Tips for Deep Learning in Biology

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Reads simulator

A fast whole-genome aligner based on de Bruijn graphs

Bayesian genotyper for structural variants

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

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