Kinghorn Centre for Clinical Genomics

ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

rageseq

RAGE-seq scripts

seave

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.

introme

seave-databases-annotations

SQL files required to set up the Seave database schema and scripts to import data from annotation sources into the Seave MySQL annotation databases.

vcfscope-measure

Measure the performance of a genomic analysis pipeline

fast5_fetcher

A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency

homebrew-genomics

Genomics formulae for the Homebrew package manager, brew.sh

phenomics-devops

Phenomics code and Jenkins dev-ops setup

phenomics-hippo

The Monarch HIPPO: Deriving insight from the medical literature by fuzzy semantic searches over diseases and phenotypes.

seave-documentation

Documentation for how to use and administrate a Seave installation.

phenomics-affinity

Affinity is a service equipped with Lucene and Luwak for active ontology search hits

phenomics-annotation-pipeline

Phenomics annotation and search suite

phenomics-notification

phenomics-pubmed-ingestion

Amazon Lambda function to fetch, clean and dispatch latest pubmed articles for annotation.

phenomics-subscription-worker

A java dcokerized runnable scheduled to perform subscribed searches and send notifications

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

genomics-r-intro

Intro to R and RStudio for Genomics

kccg-dx-igvserver

IGV server for DNAnexus data

POREquality

This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.

refynr

KCCG's cloud-based, genome analysis pipeline

shell-genomics

TxDb.Hsapiens.UCSC.hg19.ccdsGene

Annotation database generated from UCSC, using CCDS (Consensus CDS IDs)

vcfscope-asset

dx Asset bundle, supporting VCFscope

vcfscope-reporter

VCFscope report generation app.

wrangling-genomics