Repositories list

• automate_demultiplex

  Public
  Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics

  workstationpipelinesdemultiplexing+ 1dnanexus-sdk

  Python

  •

  Other

  •2•1•14•0•Updated Dec 25, 2024Dec 25, 2024

• mokabed

  Public
  Generates BED files

  Python

  •0•0•13•0•Updated Dec 20, 2024Dec 20, 2024

• bedmakerGUI

  Public
  Python

  •0•0•1•0•Updated Dec 19, 2024Dec 19, 2024

• workstation_crontab

  Public
  0•0•1•0•Updated Dec 16, 2024Dec 16, 2024

• fhprs

  Public
  FH Polygenic risk score

  polygenic-risk-scores

  Python

  •0•0•1•0•Updated Dec 9, 2024Dec 9, 2024

• SNP_haplotyper

  Public
  BASHer (BiAllellic SNP Haplotyper). This script filters and classifies SNPs for SNP Array data

  arrays

  Python

  •0•0•1•3•Updated Nov 28, 2024Nov 28, 2024

• dnanexus_ED_readcount_analysis

  Public
  This app calculates the readcount for a batch of samples for CNV calling using ExomeDepth.

  cnvdnanexus

  Shell

  •0•0•2•0•Updated Nov 20, 2024Nov 20, 2024

• sophiaCLI_automate

  Public
  AOI script for automation of Sophia CLI requests

  Python

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• dnanexus_mokapipe_workflow

  Public
  Workflow description of DNANexus workflow GATK3.5

  0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• dnanexus_happy

  Public
  DNAnexus app comparing a query VCF to a truth VCF to calculate performance metrics including sensitivity and precision using hap.py and vcfeval

  Shell

  •0•0•2•0•Updated Nov 13, 2024Nov 13, 2024

• archer_api_upload

  Public
  Shell

  •

  MIT License

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• dnanexus_scip_mpileup

  Public
  Modified version of dnanexus_mpileup to do some extra data manipulation on scip patient data

  Shell

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• SCIP

  Public
  0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• dnanexus_ED_cnv_calling

  Public
  Performs CNV calling using ExomeDepth.

  cnvdnanexus

  Shell

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

• adhoc_scripts

  Public
  Scripts for adhoc changes. See readme for details of each script

  Python

  •0•0•3•0•Updated Oct 31, 2024Oct 31, 2024

• get_DNAnexus_URLs

  Public
  Generates a .json containing URLs for VCF, BAM and index files located on DNAnexus for use in the IGV browser

  igv

  Python

  •0•0•3•0•Updated Oct 8, 2024Oct 8, 2024

• dnanexus_archer_api_upload

  Public
  MIT License

  •0•0•0•1•Updated Oct 1, 2024Oct 1, 2024

• igvwebapp

  Public
  Docker build for the IGV WebApp

  JavaScript

  •0•0•2•0•Updated Sep 4, 2024Sep 4, 2024

• dMLPA-flask

  Public
  Flask frontend to dMLPA dockerised R Scripts

  Python

  •0•0•0•1•Updated Aug 19, 2024Aug 19, 2024

• integrity_checking

  Public
  Script to display a message box on the sequencers, with the goal of ensuring data is not lost should the data integrity check fail

  Python

  •0•0•2•0•Updated Aug 9, 2024Aug 9, 2024

• dnanexus_duty_csv

  Public
  DNAnexus implementation of duty_csv. To be used in conjunction with process_duty_csv

  dutydnanexus

  Shell

  •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

• duty_csv

  Public
  Generates a CSV file containing DNAnexus download links for end of run processing. To be used in conjunction with process_duty_csv

  duty

  Python

  •0•0•3•0•Updated Jul 10, 2024Jul 10, 2024

• moka-fe

  Public
  This repo is incomplete and serves as a backup of some code from Moka. It includes some legac(hitt)y code.

  Python

  •4•0•0•0•Updated Jul 9, 2024Jul 9, 2024

• workstation_housekeeping

  Public archive
  Scripts to manage data on the NGS workstation

  workstation

  Python

  •

  Other

  •1•0•10•1•Updated Jul 5, 2024Jul 5, 2024

• dnanexus_arraybackup

  Public
  Upload files from the MicroArray scanner PC to DNANexus

  Python

  •0•0•1•0•Updated Jul 5, 2024Jul 5, 2024

• samplesheet_validator

  Public
  A package to validate the formatting of Illumina SampleSheets and which notifies the user of any issues

  samplesheetvalidation-tool

  Python

  •

  Other

  •0•0•2•0•Updated Jun 27, 2024Jun 27, 2024

• dnanexus_upload_multiqc

  Public
  App to upload multiqc files to genomics server

  uploaderdnanexus

  Shell

  •1•0•3•1•Updated Jun 25, 2024Jun 25, 2024

• dnanexus_oncodeep_upload

  Public
  Shell

  •0•0•1•0•Updated Jun 19, 2024Jun 19, 2024

• archer_archiving

  Public
  Script for backing up data from the Archer analysis platform to DNAnexus for long term storage

  Python

  •0•0•1•0•Updated Jun 13, 2024Jun 13, 2024

• dnanexus_swiss_army_SNP_bcftools_filter

  Public
  This repository contains the commands executed by the swiss army knife app (v3.0.0) to format a VCF according to GeL specifications for SNP ID checks

  Shell

  •0•1•1•0•Updated Jun 10, 2024Jun 10, 2024