moka-guys/SNP_haplotyper

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

Language: Python - Size: 32.9 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

moka-guys/oncodeep_upload

Size: 12.7 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

moka-guys/validation

Scripts and workflows to perform NGS validations

Language: Makefile - Size: 35.2 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

moka-guys/samplesheet_validator

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

Language: Python - Size: 92.8 KB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

moka-guys/archer_archiving

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

Language: Python - Size: 43 KB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0

moka-guys/ngrok_start

Allow SSH access to the system by running ngrok as a background process

Language: Shell - Size: 17.6 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 0

moka-guys/automate_demultiplex

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

Language: Python - Size: 668 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 1 - Forks: 2

moka-guys/workstation_housekeeping

Scripts to manage data on the NGS workstation

Language: Python - Size: 92.8 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 1

moka-guys/fhprs

FH Polygenic risk score

Language: Python - Size: 52.7 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

moka-guys/trend_analysis

A script to create per test type and per sequencer trend analysis reports using MultiQC output files.

Language: Python - Size: 474 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/SNP_genotyping 📦

OBSOLETE - unlikely to have any benefit over using hap.py. In-house sample matching service - may become useful if we stop sanger confirming and use SNPS instead for sample ID

Size: 13.7 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

moka-guys/seglh-toolbox

Source code for third party tools that have been verified/validated for use, as docker images

Language: C - Size: 13.7 KB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

moka-guys/seglh-naming

SEGLH naming schemes

Language: Python - Size: 70.3 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

moka-guys/process_duty_csv

This repository contains the script for processing Duty CSVs on Trust Windows PC

Language: Python - Size: 40 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/multiqc_plugins

MultiQC modules for custom software and pipeline QC metrics at the SEGLH

Language: Python - Size: 52.7 KB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 0 - Forks: 1

moka-guys/GeL2MDT Fork of NHS-NGS/GeL2MDT 📦

OBSOLETE as 100KGP is complete. Repository for GeL2MDT, management software for 100KGP patient results and MDTs.

Language: JavaScript - Size: 12.4 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

moka-guys/dx_api_bridge

DNAnexus API bridge. Retrieve data object URIs. Manage archival processes and perform cost audits.

Language: Python - Size: 69.3 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

moka-guys/duty_csv

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

Language: Python - Size: 133 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_tso500_output_parser 📦

DNAnexus app to set off QC steps (DNAnexus apps) for specific files output by the TSO500 app

Language: Shell - Size: 12.7 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_tso500

Runs the Illumina TSO500 local analysis app

Language: Shell - Size: 20.5 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_qiagen_upload

App to upload TSO500 samples to Qiagen

Language: Shell - Size: 6.84 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_multiqc

DNAnexus app running MultiQC to generate run wide quality control (QC) using the outputs from MokaAMP, MokaPipe and MokaWES pipelines

Language: Shell - Size: 3.96 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 1

moka-guys/dnanexus_mokapipe_workflow

Workflow description of DNANexus workflow GATK3.5

Size: 27.3 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_MokaCAN_workflow 📦

Workflow description of DNANexus workflow MokaCAN

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_mokaonc_workflow 📦

Workflow description of DNANexus workflow MokaONC. Replaced by MokaAMP

Language: Shell - Size: 25.4 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_duty_csv

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

Language: Shell - Size: 39.1 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_ED_cnv_calling

Performs CNV calling using ExomeDepth.

Language: Shell - Size: 26.4 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_arraybackup

Upload files from the MicroArray scanner PC to DNANexus

Language: Python - Size: 73.2 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/coverage_boxplots

CovApp is an R shiny app that shows gene coverage boxplots for in-house WES data. In production use but no release / audit

Language: Python - Size: 10.2 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

moka-guys/ArraySpiker

Script run during the analysis of Agilent CGH Array results. It compares the expected presence of spiked in probes to that detected, flagging any mismatch to the user

Language: Python - Size: 23.4 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_MokaSNP_workflow 📦

OBSOLETE: Workflow description of DNANexus workflow 'SNP Genotyping' (genotypes a set of SNPs to be uploaded to the sample matching service for the GMS WGS)

Size: 8.79 KB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_mokawes_workflow 📦

OBSOLETE: Workflow description of DNANexus workflow MokaWES

Size: 25.4 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/seglh-cnv

Scripts and docker images to run CNV pipelines

Language: R - Size: 251 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 3 - Forks: 1

moka-guys/MultiQC Fork of MultiQC/MultiQC 📦

Aggregate results from bioinformatics analyses across many samples into a single report.

Language: Python - Size: 20.1 MB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

moka-guys/moka_to_genapp 📦

OBSOLETE: 100KGP script. ssh's onto the genapp server and runs gel_report.py script on genapp server

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

moka-guys/100k_moka_variants 📦

Language: Python - Size: 44.9 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_amplivar_coverage 📦

OBSOLETE: DNAnexus app running a Python script which parses output from amplivar and variant calling steps into one document per sample

Language: Python - Size: 240 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

moka-guys/mokapapp 📦

OBSOLETE: Never used. Import GeL PanelApp panels into Moka

Size: 56.6 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

moka-guys/summarise_gene_panel 📦

OBSOLETE: One-off research project, summarising coverage of a set of genes

Size: 1.95 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

moka-guys/CIP_API_Reports 📦

Language: Python - Size: 466 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

moka-guys/moka-fe

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

Language: Python - Size: 1.8 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 4

moka-guys/helpdesk 📦

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 1 - Forks: 3

moka-guys/dnanexus_mpileup

Language: Python - Size: 2.25 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/dMLPA-flask

Flask frontend to dMLPA dockerised R Scripts

Language: Python - Size: 789 KB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_bcl2fastq2

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/qiagen_upload

Language: Python - Size: 32.2 KB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

moka-guys/custom_reference

Size: 5.86 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/PanelApp_API 📦

Accesses the panelapp API and returns two files containing a list of gene symbols and ensembl ids for each gene panel

Language: Python - Size: 85 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

moka-guys/mpileup_coverage

To be used for SCIP. Produces a coverage report that represents the coverage available to varscan

Language: Python - Size: 4.88 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_mpileup_coverage

To be used for SCIP. DNAnexus app calculating whether each amplicon is covered sufficiently - represents the coverage available to varscan. Runs script from moka-guys/mpileup_coverage

Language: Shell - Size: 4.88 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_BWA

SUPERSEDED BY SENTIEON. DNAnexus app mapping FASTQ reads (paired or unpaired) to a reference genome with the BWA-MEM algorithm

Language: Shell - Size: 517 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_convert_to_RPKM_bedfile 📦

SUPERSEDED BY EXOME DEPTH. DNANexus app creating bedfiles suitable for use with the DNA nexus RPKM app

Language: Shell - Size: 5.86 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_RPKM 📦

SUPERSEDED BY EXOME DEPTH. DNAnexus app that uses moka-guys/RPKM to perform RPKM analysis

Language: Shell - Size: 71.3 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/RPKM 📦

SUPERSEDED BY EXOME DEPTH. Tools used to generate RPKM data from BAM files. Makes use of Conifer CF_bam2RPKM function to generate RPKM. Contains a wrapper script called rpkmanalysis.py which processes a list of BAMs and outputs RPKM text files to a specific output folder.

Language: Python - Size: 31.3 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_ampliconfilter 📦

NO LONGER IN PROD USE. DNAnexus app running AmpliconFilter v1.0 to remove any alignments which are not the product of an amplicon

Language: Shell - Size: 505 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/ampliconfilter 📦

NO LONGER IN PROD USE. Scripts to mask or softclip primers in aligned DNA amplicons

Language: Python - Size: 153 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_mokaamp_workflow 📦

NO LONGER IN PROD USE. Workflow description of DNANexus workflow MokaAMP

Size: 40 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_varscan2 📦

NO LONGER IN PROD USE. DNAnexus app applying Varscan2 (v2.4.3), a variant caller well suited for somatic samples

Language: Shell - Size: 20 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_vardict 📦

NO LONGER IN PROD USE. DNAnexus app performing variant calling using the VarDict variant caller, calling SNV, MNV, indels (<120 bp default), and complex variants

Language: Perl - Size: 6.83 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_normals_readcount_analysis

The app creates a panel of normals for Exomedepth

Language: Shell - Size: 6.84 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/FlaskTemplate

Cookiecutter template to allow developers to quickly create a simple web tool ready for attaching to backend code.

Language: Python - Size: 807 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/SNP_array_transition_211220

Various scripts for use with the array software

Language: Python - Size: 107 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

moka-guys/integrity_checking

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

Language: Python - Size: 41.5 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

moka-guys/benchmarking_tool

Django benchmarking tool webapp

Language: Python - Size: 480 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

moka-guys/vcfserver

VCF HTTP server

Language: Python - Size: 11.7 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

moka-guys/undocking

Tools to backup and move images from dockerhub

Size: 12.7 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

moka-guys/_CNVkit_DNAnexus_App

Part of MSc project for Igor

Size: 3.91 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

moka-guys/batch_VCF_verifier 📦

Compares a batch of truth VCFs to a batch of query VCFs to verify genomic pipelines

Size: 3.91 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

moka-guys/guidance

Guidance documents that cover coding style, versioning, and documentation of code written in the bioinformatics groups of the London South Genomic Laboratory Hub

Language: Shell - Size: 281 KB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

moka-guys/dMLPA-reporting

Report generator for dMPLA

Size: 67.4 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_bigwig_coverage_map_report

DNA Nexus App to create bigwig coverage maps from the stiched/realigned BAMs for TSO runs

Size: 18.6 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_batch_runner 📦

Language: Shell - Size: 3.91 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_run_single_app 📦

Language: Python - Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/arraypgd 📦

Language: Python - Size: 117 KB - Last synced: about 1 month ago - Pushed: over 10 years ago - Stars: 0 - Forks: 0

moka-guys/cgh-processor Fork of techblue/cgh-processor 📦

Array CGH Signal processor

Language: Java - Size: 360 KB - Last synced: about 1 month ago - Pushed: about 10 years ago - Stars: 0 - Forks: 0

moka-guys/ngs 📦

Language: Python - Size: 739 KB - Last synced: about 1 month ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0

moka-guys/genetic_variant_interpretation_tool Fork of jeffkleinberger12/genetic_variant_interpretation_tool 📦

html file for variant interpretation

Language: JavaScript - Size: 13.7 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/arraybed 📦

Size: 164 KB - Last synced: about 1 month ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

moka-guys/geneonlycoverage 📦

Language: Python - Size: 168 KB - Last synced: about 1 month ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_GATK_diagnose_targets 📦

Language: Shell - Size: 5.89 MB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/overlapping_genes 📦

Language: Python - Size: 5.86 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_qualimap 📦

Language: R - Size: 28.9 MB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/LeemaExomes 📦

Language: Python - Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/swift_scripts 📦

Scripts used to set off amplivar

Language: Perl - Size: 3.91 KB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_concat_fastqs 📦

Language: Python - Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/ngtransition 📦

Scripts associated with converting pipeline over from using NextGene utilities

Language: Python - Size: 8.79 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/161216_rerun_coverage_sambamba 📦

Size: 1.95 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_gatk_haplotypecaller 📦

Language: Shell - Size: 8.79 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_picard 📦

Language: Shell - Size: 5.52 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

moka-guys/mokapipe_v2.9_validation 📦

Language: HTML - Size: 674 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_mokavendor 📦

Language: Shell - Size: 1.07 MB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_workflows 📦

Size: 8.79 KB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

moka-guys/fastq_contaminator 📦

Creates a fastq file simulating a cross-contaminated sample by combining the fastq files from two samples.

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_automate_multiqc_workflow 📦

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

moka-guys/penetrance 📦

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

moka-guys/gatk_v3.5 📦

This contains dnanexus-made apps that predate existing version control/audit systems

Language: R - Size: 47 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_minimap2_nanopore 📦

Language: Shell - Size: 1.95 MB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_albacore_barcoding 📦

Language: Shell - Size: 5.86 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_gatk_variantannotator 📦

Language: Shell - Size: 5.9 MB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

moka-guys/dnanexus_nanopore_HTT_repeat_counting_workflow 📦

Size: 1.95 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0