Repositories list

• ACCESS-Pipeline

  Public
  cfDNA Sequencing Pipeline with UMI

  cancer-genomics

  Python

  •

  MIT License

  •3•10•38•14•Updated Feb 12, 2025Feb 12, 2025

• igo-run-qc-node

  Public
  JavaScript

  •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• neoantigen-pipeline

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

  Python

  •

  MIT License

  •0•1•10•1•Updated Feb 12, 2025Feb 12, 2025

• smile-message-publisher

  Public
  Spring Boot LIMS SampleMetadata publisher framework

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•1•Updated Feb 12, 2025Feb 12, 2025

• beagle

  Public
  Voyager Backend

  Python

  •5•2•97•20•Updated Feb 12, 2025Feb 12, 2025

• igo-genomics

  Public
  Vue

  •0•1•3•0•Updated Feb 11, 2025Feb 11, 2025

• forte

  Public
  Functional Observation of RNA Transcriptome Elements/Expression

  Nextflow

  •

  MIT License

  •0•7•24•2•Updated Feb 11, 2025Feb 11, 2025

• ridgeback

  Public
  Toil API

  Python

  •2•1•38•4•Updated Feb 10, 2025Feb 10, 2025

• igo-sample-submission-node

  Public
  Sample Submission API written in node.js

  JavaScript

  •1•0•1•31•Updated Feb 10, 2025Feb 10, 2025

• smile-server

  Public
  Java

  •4•2•72•2•Updated Feb 7, 2025Feb 7, 2025

• igo-demux

  Public
  Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelines

  Python

  •

  Apache License 2.0

  •0•6•4•1•Updated Feb 7, 2025Feb 7, 2025

• loki

  Public
  Workflow for handling CNV events

  Nextflow

  •

  MIT License

  •1•1•1•0•Updated Feb 6, 2025Feb 6, 2025

• argos-cwl

  Public
  A portable and reproducible pipeline for targeted analysis

  Common Workflow Language

  •0•0•4•2•Updated Feb 6, 2025Feb 6, 2025

• LimsRest

  Public
  the restful service used by the IGO LIMS

  Java

  •2•2•5•4•Updated Feb 6, 2025Feb 6, 2025

• argos-bam

  Public
  The CWL bam generator for ARGOS, separated into its own repo

  Common Workflow Language

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• 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 6, 2025Feb 6, 2025

• beagle_cli

  Public
  Beagle API Command Line Utility

  Python

  •1•0•8•3•Updated Feb 5, 2025Feb 5, 2025

• igo-lims-plugins

  Public
  Sapio LIMS customizations to workflows for IGO

  Java

  •0•2•1•7•Updated Feb 5, 2025Feb 5, 2025

• igo-landing-page

  Public
  JavaScript

  •1•0•0•6•Updated Feb 5, 2025Feb 5, 2025

• igo-sample-qc-node

  Public
  Sample QC with nodejs backend

  JavaScript

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• tempo

  Public
  CCS research pipeline to process WES and WGS TN pairs

  Groovy

  •5•12•48•9•Updated Feb 3, 2025Feb 3, 2025

• smile-request-filter

  Public
  CMO MetaDB Request Filter app

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• smile-messaging-java

  Public
  CMO Messaging Library

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• smile-commons

  Public
  Centralized configurations for checkstyle plugin and dependency management.

  Java

  •

  GNU Affero General Public License v3.0

  •5•1•0•0•Updated Jan 29, 2025Jan 29, 2025

• igo-delivery

  Public
  Delivery email, symlinks and permissions for IGO projects

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• smile-dashboard

  Public
  TypeScript

  •

  GNU Affero General Public License v3.0

  •8•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• argos-docs

  Public
  Working repo for Argos pipeline documentation

  0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• smile-databricks-gateway

  Public
  Go

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• mskprotobuf

  Public
  Repository for storing protocol buffer definitions and generated code

  Shell

  •1•1•0•1•Updated Jan 16, 2025Jan 16, 2025

• test

  Public
  Testing transfer functionality between accounts

  0•0•1•0•Updated Jan 16, 2025Jan 16, 2025