Clinical Genomics

scout

VCF visualization interface

genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.

BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

stranger

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

cg

Glue between Clinical Genomics apps

loqusdb

A simple observation count database

trailblazer

Keep track of and manage analyses

raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇

reference-files

Small reference files

cg_lims

microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

chanjo2

Persistent coverage analysis tool using the d4 format

housekeeper

File data orchestrator

crunchy

Compress fastq files with spring and check the integrity

gens

hermes

Communication layer between CG and the pipelines.

preClinVar

A ClinVar API submission helper written in FastAPI

snippets

Code snippets and one liners

udni-tip2toe

UDNI tip2toe deep phenotyping frontend

genotype-api

Rewrite of genotype package

Janus

Repository to collect, parse and ship of multiqc data from housekeeper to cg.

MUTANT

Microbial Utility Toolbox And wrapper for data traNsmission and Transformation

snippet_dev

short-read Non-Invasive Prenatal pipeline examination Tool

TestRepo_Remove-

short-read Nono-Invasive Prenatal pipeline evaluation Tool

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

cg-mockapi

chanjo-report

Report generator for Chanjo output

schug

All you need to know about genes, transcripts and exons