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    194 repositories

    • automate_demultiplex

      Public
      Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
      workstationpipelinesdemultiplexingdnanexus-sdk
      Python
      •
      Other
      •2•1•16•0•Updated Jun 10, 2025Jun 10, 2025

    • 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 9, 2025Jun 9, 2025

    • bedmakerGUI

      Public
      Python
      •0•0•1•0•Updated Jun 4, 2025Jun 4, 2025

    • SNP_haplotyper

      Public
      BASHer (BiAllellic SNP Haplotyper). This script filters and classifies SNPs for SNP Array data
      arrays
      Python
      •0•0•1•5•Updated Jun 2, 2025Jun 2, 2025

    • dx_command_generator

      Public
      CLI tool for generating run commands in CP2 workflows
      Python
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • mokabed

      Public
      Generates BED files
      Python
      •0•0•13•0•Updated May 8, 2025May 8, 2025

    • 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 Apr 24, 2025Apr 24, 2025

    • pre_basher_filter

      Public
      MIT License
      •0•0•0•1•Updated Apr 15, 2025Apr 15, 2025

    • dnanexus_mokapipe_workflow

      Public
      Workflow description of DNANexus workflow GATK3.5
      0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • sophiaCLI_automate

      Public
      AOI script for automation of Sophia CLI requests
      Python
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • SCIP_preprocessing

      Public
      Preprocessing of data for SCIP runs, from FASTQs to mpileup files
      0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • seglh-naming

      Public
      SEGLH naming schemes
      Python
      •
      Apache License 2.0
      •1•1•2•0•Updated Feb 17, 2025Feb 17, 2025

    • SCIP_DNAnexus

      Public
      DNAnexus app which runs the SCIP python script in a docker container, predicting fetal sickle cell status and outputting an HTML report
      0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • SCIP

      Public
      0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • dnanexus_ED_cnv_calling

      Public
      Performs CNV calling using ExomeDepth.
      cnvdnanexus
      Shell
      •0•1•4•1•Updated Feb 11, 2025Feb 11, 2025

    • dnanexus_normals_readcount_analysis

      Public
      The app creates a panel of normals for Exomedepth
      cnvdnanexus
      Shell
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • 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 Feb 4, 2025Feb 4, 2025

    • 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

    • 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

    • 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 B33F 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

    • 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
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