Top 274 genomics open source projects

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

Predict plasmids from uncorrected long read data

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

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Inference of switch-like differential expression along single-cell trajectories

Find causal cell-types underlying complex trait genetics

Home of the Genomic Feature and Variation Ontology (GFVO)

An ontology of cell types

Introduction to Cloud Computing for Genomics

A curated list of awesome bioinformatics software.

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

Fast alignment and preprocessing of chromatin profiles

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

Assembling the cause of phenotypes and genotypes from NGS data

Provide R access to the NCI Genomic Data Commons portal.

An open-access bioinformatics text

Genetic Map Comparison

Feature Annotation Location Description Ontology

Bystro genetic analysis (annotation, filtering, statistics)

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Version 2.1.0 released

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Compute N50/NG50 and auN/auNG

(WIP) best-practices workflow for rare disease

A package for designing compact and comprehensive capture probe sets.

Complex structural variant detection from WGS data

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

Fast hash function for DNA sequences

echt rapid variant annotation and filtering

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.

Data Wrangling and Processing for Genomics

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

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

An interactive web portal for exploring immuno-oncology data

PERF is an Exhaustive Repeat Finder

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

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

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

Toolkit for preparing genomes for submission to NCBI

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

A faster lmm for GWAS. Supports GPU backend.

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

My collection of light bioinformatics analysis pipelines for specific tasks

Chanjo provides a better way to analyze coverage data in clinical sequencing.

A modular annotation tool for genomic variants

Environmental DNA metabarcoding taxonomic identification

pythonic wrapper for htslib

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Clustering scRNAseq by genotypes

A proof of concept of RNAseq pipeline

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Learn interpretable computational phenotyping models from k-merized genomic data

mgatk: mitochondrial genome analysis toolkit

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Interactive assembly and analysis of RAD-seq data sets

Grammar of Scalable Linked Interactive Nucleotide Graphics