Clinical Genomics

chanjo

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

stranger

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

genotype

Simple genotype comparison of VCF files

demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

clinical_EPPs

EPPs used in clinical genomics LIMS

fluffy

FetaL AneUploidy and FetalFraction analYsis Pipeline

backup

Fluffy_nextflow

A nextflow pipeline to run Fluffy

statina

cglims

LIMS interface for the specific usage at Clinical Genomics

crunchy

Compress fastq files with spring and check the integrity

orderportal

Clinical genomics web interface for placing orders

varg

variant validation report generator

genotype-api

Rewrite of genotype package

MUTANT

Microbial Utility Toolbox And wrapper for data traNsmission and Transformation

bump2version-ci

Repository to host automated bump2version CI to run on python repositories

cgmodels

Models and contracts used at clinical genomics

cgstats

Models and connecting to clinstatsdb

chanjo-report

Report generator for Chanjo output

chromograph

Genetics graphing tool

flask-ldapconn

Flask extension providing python-ldap3 connection and ORM for accessing LDAP servers.

limsmock

File-based mock for the lims REST API. For testing.

MegaFusion

Convert RNA fusion files to SV VCF

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

primer-schemes

Primer schemes used by Clinical Genomics Stockholm

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

Scout-REViewer-service

A rest service for generating REViewer output.

SOUP-Library

taxpasta

TAXnomic Profile Aggregation and STAndardisation

test-datasets

Test data to be used for automated testing with the nf-core pipelines