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Dataleverans

Vi levererar data på flera sätt för olika typer av applikationer.

Scout-analys

Kan göras för både helgenoms-prover och exom-prover. Efter sekvensering analyseras data i MIP, en pipeline utvecklad på CMMS (Karolinska Institutet) med inriktning på diagnos av monogena, ärftliga sjukdomar. Läs mer i den officiella dokumentationen för MIP (analyspipeline).

Standardleveransen av resultat från sekvensering och analys sker genom uppladdning av annoterade och rankade varianter till vårt visualiseringsverktyg Scout. Kontakta oss för att diskutera access till denna tjänst. Kontakta oss

Scout Variants

Rådata-leverans

Vi levererar rådata från sekveneringsinstrumenten (FASTQ-filer). Leveranserna sker i första hand till en server men kan även göras via hårddiskar (för en extra kostnad).

Mikrobiell analys

För mikrobiella prover görs en QC-analys av proverna som levereras tillsammans med rådata-leveransen (FASTQ-filer). Vi har även en typnings-pipeline, microSALT som bestämmer ett provs organism-specifika sekvenstyp och dess resistensmönster.

Cancer-analys

Se engelska versionen, klicka här

Kontakta oss för mer information om access till våra olika tjänster.


Data delivery

We deliver data in different ways for different types of applications.

Scout analysis

Applicable to both whole genome and exome samples. After sequencing the data is analysed using MIP, a pipeline developed by CMMS(Karolinska Institutet) focusing on diagnosis of monogenic, hereditary diseases. Read more in the official documentation for MIP (analysis pipeline).

The standard delivery of the results from sequencing and MIP analysis happens through uploading of annotated and ranked variants to our visualisation tool Scout. Contact us for discussion about access to this service.

Scout Variants

Raw data delivery

We deliver raw data from sequencing (FASTQ files). Deliveries are done firstly to our delivery server, but can also be made via external hard drives to an additional cost.

Microbial analysis

For microbial samples a QC analysis report is delivered together with the raw data (FASTQ files). We also have a typing pipeline microSALT that determines a sample's organism specific sequencing type and it's resistance pattern.

Cancer analysis

We have an analysis pipeline for somatic mutations in cancer that can analyse both tumor/normal pairs and tumor only samples, BALSAMIC. From this application we deliver below files. The italic files are created for Target genome analysis (TGA) and Whole Exome Sequencing (WES) analysis only. Files in bold are created for Whole Genome Sequencing (WGS) only.

  • VarDict: VEP annotated vcf-file with somatic and small INDEL SNVs
  • TNscope: VEP annotated vcf-file with somatic and small INDEL SNVs
  • TNhaplotyper: VEP annotated vcf-file with somatic and small INDEL SNVs
  • Manta: VEP annotated vcf-file with somatic structural variants and large INDELs SNVs
  • CNVkit: VEP annotated vcf-file with somatic copy number variations (CNV)
  • *diagram.pdf: Diagram of all chromosomes illustrating gain and losses
  • *scatter.pdf: Scatter of all chromosomes illustrating gain and losses
  • *cnr: Value of loss/gain for each segment. E.g. log2(3/2)=0.6 will indicate duplication of one allele for that region. log2(1/2)=-1 indicates loss/deletion of one allele for that region.
  • cram: Sequencing alignment data (compressed version of bam-file).
  • fp.fastq.gz: quality trimmed fastq-file used in BALSAMIC analysis
  • multiqc_report.html: Includes all qc-values from the analysis (duplication rate, on-target, coverage, etc)

Contact us for more information about access to our different services.