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

Data intensive science for everyone.

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

Scalable genomic data analysis.

Script to automatically create and run IGV snapshot batchscripts

Scripts to download genomes from the NCBI FTP servers

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Pan-genome wide association studies

C++ library and cmdline tools for parsing and manipulating VCF files

A tool to circularize genome assemblies

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

A fast whole-genome aligner based on de Bruijn graphs

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Ultra-fast and memory-efficient (meta-)genome assembler

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

Efficient pythonic random access to fasta subsequences

NGLess: NGS with less work

An open source platform for managing and analyzing biomedical big data

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

Fast alignment and preprocessing of chromatin profiles

nim wrapper for htslib for parsing genomics data files

annotate a VCF with other VCFs/BEDs/tabixed files

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

Fast genome-wide functional annotation through orthology assignment

A cool place to store your Hi-C

PHANOTATE: a tool to annotate phage genomes.

Development repository for the Bioconductor package 'mixOmics '

Detection of NCLDV signatures in 'omic data

Tools to work with variant call format files

Framework for building fast genomics web tools with WebAssembly and WebWorkers

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

Assembling the cause of phenotypes and genotypes from NGS data

De novo assembly based variant calling pipeline for Illumina short reads

variant expressions, annotation, and filtering for great good.

Earl Grey: A fully automated TE curation and annotation pipeline

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

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

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

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

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

A collection of scripts and notes related to genomics and bioinformatics

Home of the Genomic Feature and Variation Ontology (GFVO)

RADseq Data Exploration, Manipulation and Visualization using R

Introduction to Cloud Computing for Genomics

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

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

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

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

Antimicrobial Resistance Identification By Assembly

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Provide R access to the NCI Genomic Data Commons portal.

An open-access bioinformatics text

Genetic Map Comparison

AQUAS TF and histone ChIP-seq pipeline

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

Feature Annotation Location Description Ontology

Bystro genetic analysis (annotation, filtering, statistics)

GCP Essentials for Bioinformatics Researchers

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