301 Open source projects that are alternatives of or similar to Viral Ngs

Genomic Data Retrieval with R

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

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.

Official code repository for GATK versions 4 and up

PERF is an Exhaustive Repeat Finder

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

A genome browser that shows long reads and complex variants better

A package for designing compact and comprehensive capture probe sets.

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

GenomeTools genome analysis system.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

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

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

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

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

Bayesian genotyper for structural variants

Bayesian haplotype-based mutation calling

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

An interactive web tool for quality control of DNA sequencing data

🌈Scaffold genome sequence assemblies using linked read sequencing data

An R package for creating Q-Q and manhattan plots from GWAS results

A friendly next-generation interface for Genomic data discovery powered by InterMine

Model and predict short DNA sequence features with neural networks

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

MISO: An open-source LIMS for NGS sequencing centres

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

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Genomics Extension for SQLite

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

Script to automatically create and run IGV snapshot batchscripts

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Pan-genome wide association studies

A tool to circularize genome assemblies

A fast whole-genome aligner based on de Bruijn graphs

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

NGLess: NGS with less work

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

nim wrapper for htslib for parsing genomics data files

A collaboratively written review paper on deep learning, genomics, and precision medicine

A cool place to store your Hi-C

Development repository for the Bioconductor package 'mixOmics '

Tools to work with variant call format files

variant expressions, annotation, and filtering for great good.

Framework for building fast genomics web tools with WebAssembly and WebWorkers

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

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Simulate genealogical trees and genomic sequence data using population genetic models

Analysis pipelines for sequencing data

A collection of scripts and notes related to genomics and bioinformatics

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

RADseq Data Exploration, Manipulation and Visualization using R

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

Genome annotation with AUGUSTUS

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A list of web-based interactive biological data visualizations.

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

Antimicrobial Resistance Identification By Assembly

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

A versatile pairwise aligner for genomic and spliced nucleotide sequences