Resources
The CG platform has access to specialized equipment and analytical frameworks that enable us to introduce new high-throughput techniques into healthcare.
Equipment
We continuously explore emerging genomics technologies to facilitate the integration of genomics-based precision diagnostics and precision medicine in Sweden. Please note that only relevant equipment is listed and not all listed equipment is available for access service (User access service refers to a service that some nodes provide, where users, after receiving proper training and accreditation, are granted access to the equipment to operate it independently)contact us if you have any enquiries regarding our capabilities.
- Automatic robotic systems
- BRAVO NGS Workstation, Hamilton NGS Star, Beckman i5 Automated Workstation, Myra Liquid Handling Station, Magnis NGS Prep system, Tecan Fluent 480, Tecan Fluent 780
- Various systems for QC, quantification and fragment analyses
- TapeStation, Quantification using fluorescent assay (Qubit, Quantit), Agilent Fragment Analyzer, Agilent Femto Pulse
- Instrumentation for microarray analysis
- Affymetrix microarray, HiScan, NextSeq550, iScan
- Instrumentation for Sanger sequencing
- ABI 3500, ABI3500 xL
- Instrumentation for library preparation including single cell
- Mission Bio Tapestri, 10x Chromium Genomics
- Instrumentation for real time PCR and ddPCR
- BioRad qPCR, QIAcuity I, ABI QuantStudio 6, QX200 Droplet Digital PCR System, ABI 7500, ABI QuantStudio 7 flex
- Instrumentation for Multispectral imaging
- Saphyr optical mapper
- Sequencing platforms
- Illumina (iSeq, MiniSeq, MiSeq, NextSeq 500, NextSeq 550, NextSeq 550 Dx, NextSeq 2000, NovaSeq 6000, NovaSeq 6000 Dx, NovaSeq X)
- Ion Torrent (Ion S5, Ion S5 Prime, Ion Torrent PGM, Genexus system)
- Nanopore (MinION, GridION, PromethION)
- Nanostsring (GeoMx, nCounter)
- Qiagen (GeneReader)
- PacBio (Revio)
Analytical resources
Our advanced analytical pipelines undergo continuous enhancement through a national collaboration among various CG nodes, GMS, and other initiatives. Additionally, we have developed open-source bioinformatics tools for the wider research community. Here some notable examples:
Pipeline for resistance profile for Human betaherpesvirus 5 (cytomegalovirus)
Single-cell RNAseq analysis pipeline
Pipeline for Internal Tandem Duplications in the FLT3 gene
Hydra genetics (snakemake) workflow for hematological malignancies WGS
Fraggler is a Python package for fragment analysis that provides functionality for analyzing and generating reports for fsa files
Plugins to Geneious Prime for analysis of SARS-CoV-2 genomes using Nanopore sequencing
Sars-CoV-2 WGS data analysis
GUI utility for uploading sequence and metadata to the NGP
Hydra genetics (snakemake) pipeline for rare disease WES
Pipeline for resistance profile of hepatitis C virus
insilico panel coverage analyses
Pipeline to produce insilico panel coverage analyses
Single-cell RNAseq analysis pipeline
A simple observation count database to enable removal of recurrent, non-relevant genetic variation
Hydra genetics (snakemake) pipeline for inherited cancer capture panel
Pipeline to deliver methylation arrays to the storage system
Free tool (web and container) for DNA methylation array (450K and EPIC) data analysis.
Bioinformatic workflow for rare disease diagnostics, implemented in Perl.
Pipeline for typing the methicillin-resistant staphylococcus aureus
Tool that creates synthetic datasets to be used for quality control or benchmarking of bioinformatic tools and pipelines intended for variant calling of clinical variants.
Visualization of NIPT result data, mainly from Illumina VeriSeq NIPT Solution v1
Analysis pipeline for Ultra Deep Sequencing of NPM1 exon 11
Tool for detection of novel processed pseudogenes using DNA sequencing data.
Conversion files for Affymetrix TAC
A MatchMaker Exchange node.
Pipeline for pharmacogenomics analysis
Hydra genetics (snakemake) pipeline for rare disease WGS
Framework for making snakemake pipeline development easier, faster, more structured and of higher quality.
GUI tool for selecting samples for Nanopore sequencing, creating sample sheets and customized protocols
Bioinformatic workflow for rare disease diagnostics – nfcore community pipeline
RNA-seq analysis pipeline for detection gene-fusions
Pipeline fo a continual monitoring of Sars-Cov2
A browser-based tool for analysing VCFs. Functionality both for germline and somatic interpretation
cgMLST for MRSA, N. meningitidis, C. diff
The sample ID verification pipeline detects possible sample swap during the WGS workflow
Tool to annotate outfiles from ExpansionHunter with the pathologic implications of the repeat
Tool that searches transgenic insertion sites in a host genome, returns figures and a report to support these findings.
nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data.
Teloplot is a GUI utility for plotting of relative telomere lengths
Hydra genetics (snakemake) pipeline for the GMS560 capture panel
Pipeline for somatic and germline variant calling (SNV, InDels, SV and CNVs)
Pipeline for running whole genome sequencing clinical samples