Repositories list

• process_fastq

  Public
  This package will help process, merge and link fastq in user specified directory from manifest file

  Python

  •

  Other

  •0•0•0•16•Updated Nov 23, 2024Nov 23, 2024

• tempo

  Public
  CCS research pipeline to process WES and WGS TN pairs

  Groovy

  •5•12•47•8•Updated Nov 23, 2024Nov 23, 2024

• igo-demux

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

  Python

  •

  Apache License 2.0

  •0•6•4•0•Updated Nov 23, 2024Nov 23, 2024

• smile-dashboard

  Public
  TypeScript

  •

  GNU Affero General Public License v3.0

  •8•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• beagle

  Public
  Voyager Backend

  Python

  •5•2•97•18•Updated Nov 21, 2024Nov 21, 2024

• loki

  Public
  Workflow for handling CNV events

  Nextflow

  •

  MIT License

  •1•0•1•0•Updated Nov 20, 2024Nov 20, 2024

• swabnseq

  Public
  Python

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• ridgeback

  Public
  Toil API

  Python

  •2•1•38•4•Updated Nov 20, 2024Nov 20, 2024

• igo-sample-submission-node

  Public
  Sample Submission API written in node.js

  JavaScript

  •1•0•1•31•Updated Nov 19, 2024Nov 19, 2024

• argos-cwl

  Public
  A portable and reproducible pipeline for targeted analysis

  Common Workflow Language

  •0•0•5•2•Updated Nov 19, 2024Nov 19, 2024

• smile-server

  Public
  Java

  •4•2•74•2•Updated Nov 18, 2024Nov 18, 2024

• smile-databricks-gateway

  Public
  Go

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• forte

  Public
  Functional Observation of RNA Transcriptome Elements/Expression

  Nextflow

  •

  MIT License

  •0•7•21•3•Updated Nov 15, 2024Nov 15, 2024

• smile-request-filter

  Public
  CMO MetaDB Request Filter app

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• smile-label-generator

  Public
  SMILE messaging service for handling CMO label generation

  Java

  •

  GNU Affero General Public License v3.0

  •3•0•0•1•Updated Nov 15, 2024Nov 15, 2024

• smile-messaging-java

  Public
  CMO Messaging Library

  Java

  •

  GNU Affero General Public License v3.0

  •3•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• smile-commons

  Public
  Centralized configurations for checkstyle plugin and dependency management.

  Java

  •

  GNU Affero General Public License v3.0

  •4•1•0•1•Updated Nov 15, 2024Nov 15, 2024

• LimsRest

  Public
  the restful service used by the IGO LIMS

  Java

  •2•2•5•4•Updated Nov 14, 2024Nov 14, 2024

• neoantigen-pipeline

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

  Python

  •

  MIT License

  •0•1•8•0•Updated Nov 14, 2024Nov 14, 2024

• roslin-variant

  Public
  Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis

  pipelineprism

  Python

  •8•15•8•3•Updated Nov 13, 2024Nov 13, 2024

• simba

  Public
  Runs all thenextflow workflow scripts for IMPACT processing

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• odin

  Public
  Module for variant calling and maf processing

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• arrakis

  Public
  Abra realignment workflow

  Nextflow

  •

  MIT License

  •0•0•1•0•Updated Nov 13, 2024Nov 13, 2024

• igo-delivery

  Public
  Delivery email, symlinks and permissions for IGO projects

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• sif

  Public
  Nextflow workflow for handling Structural Variants

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• ngs-stats

  Public
  NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times

  HTML

  •0•1•2•1•Updated Nov 6, 2024Nov 6, 2024

• igo-lims-plugins

  Public
  Sapio LIMS customizations to workflows for IGO

  Java

  •0•2•1•7•Updated Nov 5, 2024Nov 5, 2024

• igo-landing-page

  Public
  JavaScript

  •1•0•0•6•Updated Nov 5, 2024Nov 5, 2024

• vepcheck

  Public
  Nextflow pipeline to check different vep version

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• Penguin

  Public
  ecDNA detection pipeline for MSK Sequencing Data

  Jupyter Notebook

  •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024