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 GRUS
For delivery of data we collaborate with SNIC-UPPMAX, Uppsala University's resource of high-performance computers, and sequencing data from NGI will be delivered to a project at the delivery resource "GRUS" hosted by SNIC-UPPMAX.
When a sequencing project is ready for delivery, NGI registers a new delivery project with the Swedish National Infrastructure for Computing (SNIC) and data is moved to GRUS. The principal investigator (PI) of the sequencing project will be assigned as the PI of the delivery project. The bioinformatics responsible person specified on the order will be added as a member of the delivery project, provided that this person has registered an account in SUPR. The email addresses specified when placing the order must be the same as the email addresses used for registering in SUPR. Through the SNIC User and Project Repository (SUPR) web interface, the PI can administer the delivery project and add or remove members, as well as assigning a Technical Administrator and a Proxy for the PI. Members of the delivery project are able to retrieve the data from GRUS using any of the methods described in the GRUS user guide.
Data analysis can then be performed using the UPPMAX compute clusters. For more information about SNIC-UPPMAX and how to set up a UPPNEX project for data analysis, please visit the SNIC-UPPMAX webpage
For FAQ and more information about data delivery, please visit the NGI Order Portal.
The bioinformatics support team
For more information about data delivery and the SNP&SEQ Technology platform system development and bioinformatics team, please contact us at firstname.lastname@example.org.