Sample Preparation
Sequencing
FASTQ
Read alignment
BAM
Variant calling
VCF
Variant interpretation
Reporting
Coverage analysis
How it works
Install local client application or integrate into your bioinformatics pipeline
Install local client application or integrate into your bioinformatics pipeline
Use sample quality control to analyse patient sample data locally through a MS Windows client application, a Torrent Server plugin, an Illumina BaseSpace helper app or an integrated Linux command-line application. In all instances, only the quality data is transferred to the online server to view when required, leaving all patient data safely on user hardware.
Define standard operating procedures by setting test-specific thresholds for the best practice recommended key quality metrics and perform automated coverage analysis for both technical and clinical targets
Define standard operating procedures by setting test-specific thresholds for the best practice recommended key quality metrics and perform automated coverage analysis for both technical and clinical targets
Define standard operating procedures by setting test-specific thresholds for the best practice recommended key quality metrics and perform automated coverage analysis for both technical and clinical targets. Define fail and warn thresholds for up to 60 quality metrics across all stages of the sequencing process, encapsulating data from FASTQ, BAM and VCF files. The coverage analysis can be performed for complete features as described in the BED file or sub-sections down to single bases, on average or on each strand separately. Thresholds are saved as SOPs to be enacted automatically from the client application and log the results for each analysed sample, allowing the laboratory to comply with regulatory requirements.
Capture quality data for every sample running through the sequencing process, flagging failing or warning samples and automatically determine whether a sample can proceed to interpretation
Capture quality data for every sample running through the sequencing process, flagging failing or warning samples and automatically determine whether a sample can proceed to interpretation
Capture quality data for every sample running through the sequencing process, flagging failing or warning samples and automatically determine whether a sample can proceed to interpretation. In automated command-line application, prevent these samples from progressing to interpretation. Dig deep into all parameters to monitor your laboratory and get to the root cause of quality issues.
Benchmark all results internally or to peers operating on the same platform, kit and with analogous sample types. Compare sequencers or kits over time to improve operations, and develop new workflows by comparing to validated reference data.
Benchmark all results internally or to peers operating on the same platform, kit and with analogous sample types. Compare sequencers or kits over time to improve operations, and develop new workflows by comparing to validated reference data.
Benchmark all results internally or to peers operating on the same platform, kit and with analogous sample types. Compare sequencers or kits over time to improve operations, and develop new workflows by comparing to validated reference data. Use charting to view longitudinal data for any of the more than 60 quality metrics. Ensure that the lab is consistently performing and that each part of the process is providing the expected quality.
Provide evidence of consistent QC according to EuroGentest and CAP best practice guidelines
Provide evidence of consistent QC according to EuroGentest and CAP best practice guidelines
Provide evidence of consistent QC according to EuroGentest and CAP best practice guidelines. Ensure evidence of a continuous quality management process through pulling quality reports from the software to present to auditors and accreditation bodies.
Trust your data with sample quality control, and be ready for accreditation.
Inselspital Bern successfully used sample quality control to provide the required quality data in support of their ISO 17025 accreditation.
Naomi Porret
Head of Haematological Molecular Diagnostics Laboratory, Inselspital Bern
The Euformatics team, with expertise in IT, bioinformatics and genetics, was helpful in providing validation, technical support and NGS understanding. This is not something you can get from software alone.
Read the case study on how sample quality control can be used in the accreditation process
