Data delivery

All samples sequenced at the SNP&SEQ Technology Platform are handled by a highly automated processing pipeline, which takes the samples through a series of quality-certified checks. Bioinformaticians supervise the processing and make sure that the delivered data meet our high standards in terms of data quality and yield.

The SNP&SEQ Technology Platform perform per-sample standard analyses for a number of applications and supported reference genomes. Note that only a limited number of genomes are supported. Please contact SNP&SEQ if you have requests for other genomes to include (see contact information).

  • Human Whole Genome Re-sequencing. We map the reads using BWA and perform variant calling using the GATK pipeline. The variants are annotated using databases such as dbSNP and by using SNPEff. The following files are delivered: BAM, gVCF, VCF
  • RNA-Seq. The reads are mapped against the reference and a series of tools are run to determine the quality of the data and to provide users with data that is ready to be used for subsequent analysis. For more information please see nf-core/rnaseq on GitHub
  • Sequence capture (Target resequencing). We map the reads using BWA and perform variant calling using the GATK pipeline. The variants are annotated using databases such as dbSNP and by using SNPEff. Metrics on the success of the capture are included.
  • All other sequencing projects. The following files are delivered: fastq

For additional support regarding bioinformatics analysis, please contact the SciLifeLab platform National Bioinformatics Infrastructure Sweden (NBIS).

Data delivery by DDS (Data Delivery System)

For delivery of data we use the Data Delivery System (DDS) hosted by SciLifeLab Data Centre. When a sequencing project is ready for delivery, NGI registers a new delivery project at DDS where the sequencing data is deposited. Data uploaded to DDS is securely encrypted at all times and can only be decrypted by members of the specific delivery project.

For FAQ and more information about data delivery, please visit the NGIs website: Data delivery DDS

Last modified: 2022-12-07