Repositories list

• igo-lims-plugins

  Public
  Sapio LIMS customizations to workflows for IGO

  Java

  •0•2•1•10•Updated Mar 24, 2026Mar 24, 2026

• ridgeback

  Public
  Toil API

  Python

  •

  Apache License 2.0

  •2•1•38•5•Updated Mar 24, 2026Mar 24, 2026

• igo-genomics

  Public
  Vue

  •0•1•3•0•Updated Mar 24, 2026Mar 24, 2026

• igo-delivery

  Public
  Delivery email, symlinks and permissions for IGO projects

  Python

  •

  Apache License 2.0

  •0•1•0•2•Updated Mar 24, 2026Mar 24, 2026

• beagle

  Public
  Voyager Backend

  Python

  •

  Apache License 2.0

  •6•2•99•20•Updated Mar 23, 2026Mar 23, 2026

• LimsRest

  Public
  the restful service used by the IGO LIMS

  Java

  •2•2•5•4•Updated Mar 23, 2026Mar 23, 2026

• smile-dashboard

  Public
  TypeScript

  •

  GNU Affero General Public License v3.0

  •10•0•0•1•Updated Mar 20, 2026Mar 20, 2026

• ccs_cohort_utils

  Public
  Python

  •1•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• igo-sample-submission-node

  Public
  Sample Submission API written in node.js

  JavaScript

  •2•0•1•31•Updated Mar 20, 2026Mar 20, 2026

• vcf2maf

  Public
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

  perlvcfmaf+ 2

  perlvcfmafvepisoforms

  Perl

  •

  Other

  •222•415•94•1•Updated Mar 13, 2026Mar 13, 2026

• tempo

  Public
  CCS research pipeline to process WES and WGS TN pairs

  Groovy

  •0•7•51•12•Updated Mar 4, 2026Mar 4, 2026

• beagle_cli

  Public
  Beagle API Command Line Utility

  Python

  •1•1•8•3•Updated Feb 26, 2026Feb 26, 2026

• neoantigen-pipeline

  Public
  Pipeline for computing neoantigen qualities from DNA and RNA-Seq data

  Python

  •

  MIT License

  •1•6•13•1•Updated Feb 20, 2026Feb 20, 2026

• smile-server

  Public
  Java

  •4•2•95•0•Updated Feb 20, 2026Feb 20, 2026

• facets-preview

  Public
  Load, review and adjust facets fits

  R

  •3•2•14•0•Updated Feb 18, 2026Feb 18, 2026

• smile-label-generator

  Public
  SMILE messaging service for handling CMO label generation

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• facets

  Public
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

  R

  •71•158•128•4•Updated Feb 12, 2026Feb 12, 2026

• Albany

  Public
  Mission Albany

  Python

  •1•0•0•0•Updated Feb 10, 2026Feb 10, 2026

• igo-run-qc-node

  Public
  JavaScript

  •0•0•0•1•Updated Feb 9, 2026Feb 9, 2026

• smile-client

  Public
  Python

  •1•1•0•0•Updated Jan 26, 2026Jan 26, 2026

• igo-landing-page

  Public
  JavaScript

  •1•0•0•6•Updated Jan 12, 2026Jan 12, 2026

• smile-message-publisher

  Public
  Spring Boot LIMS SampleMetadata publisher framework

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• smile-request-filter

  Public
  CMO MetaDB Request Filter app

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• smile-commons

  Public
  Centralized configurations for checkstyle plugin and dependency management.

  Java

  •

  GNU Affero General Public License v3.0

  •4•1•0•0•Updated Jan 8, 2026Jan 8, 2026

• swabnseq

  Public
  Python

  •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

• critfhirdeveloper

  Public template
  CRIT FHIR Developer Documentation

  HTML

  •

  Apache License 2.0

  •21k•0•0•1•Updated Dec 18, 2025Dec 18, 2025

• ACCESS-Pipeline

  Public
  cfDNA Sequencing Pipeline with UMI

  cancer-genomics

  cancer-genomics

  Python

  •

  MIT License

  •3•11•38•14•Updated Dec 8, 2025Dec 8, 2025

• facetflow-service

  Public
  Python

  •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

• smile-messaging-java

  Public
  CMO Messaging Library

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•1•Updated Dec 2, 2025Dec 2, 2025

• Penguin

  Public
  ecDNA detection pipeline for MSK Sequencing Data

  Jupyter Notebook

  •1•0•0•0•Updated Nov 24, 2025Nov 24, 2025