Top 274 genomics open source projects

An R framework for phylostratigraphy

Tools for analyzing 10X Genomics data

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

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

Predict AMPs in (meta)genomes and peptides

Resource of human chromosome schematics & images

find large indels (in the blind spot between GATK/freebayes and SV callers)

A fast, scalable, and accurate local ancestry method.

A tool to plot significant regions of GWAS

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Command line utility for manipulating Illumina-generated FastQ files.

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Multilocus sequence typing by blast using the schemes from PubMLST

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

🐳 Bio-dockers: dockerized bioinformatic tools

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Numerical Encoding for Human Genetic Variants

Identify phage regions in bacterial genomes for masking purposes

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Spark VCF data source implementation for Dataframes

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

WebAssembly modules for genomics

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Transcripts annotation and GO enrichment Fisher tests

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Bioconductor package for management of multi-assay data

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Nextflow basic tutorial for newbie users

Python-based UCSC genome browser snapshot-taker and gallery-maker

Big Compute Learning Labs

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

A library for manipulating bioinformatics sequencing formats in Apache Spark

Improve the quality of a denovo assembly by scaffolding and gap filling

Forward-time simulation in Python using fwdpp

Explore rearrangements and copy-number amplifications in a cancer genome

phenol: Phenotype ontology library

Bead-based single-cell atac processing

Explore gnomAD datasets on the web

A fast tool for hybrid genome assembly of long and short reads

Ultrafast sequence typing and gene detection from NGS raw reads

Examples to get started with IBM Functional Genomics Platform

Manhattan plot Generator

Analysing Capture Seq Count Data

CUT&RUN and CUT&Tag data processing and analysis

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Introduction to the Command Line for Genomics

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

ntHash implementation in Rust

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

simple viewer for variant call format using htslib

GA4GH Variation Representation Python Implementation

A secure encryption tool for genomic data

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Large genome reassembly based on Hi-C data, continuation of GRAAL