Our sequencing services

Please visit the NGI website for more in-depth information about the sequencing and genotyping technologies available at the three NGI facilities.

The SNP&SEQ Technology Platform offers next-generation DNA-sequencing (NGS) services, on Illumina sequencing instruments for a variety of different applications, including whole genome sequencing (WGS), de-novo sequencing, targeted genomic sequencing, transcriptome sequencing (RNA), sequencing of chromatin immunoprecipitated DNA (ChIP seq), bisulfite sequencing for DNA methylation analysis and more.

The facility has one NovaSeq X Plus system and one NovaSeq 6000 system. In addition he facility also has one 10X Genomics Chromium iX system for single-cell applications. For additional information on our instruments and systems, please visit the NGI website, or contact us to discuss the most suitable method for your project.

Our services include:

• technical support for project design
• quality control and measurement of the DNA concentration of all samples before sequencing
• library preparation with protocols optimal for each research project
• single-read or paired-end sequencing for several different read lengths
• bioinformatics support for human WGS with alignment and variant calling
• delivery of sequence reads with quality information to a secure delivery resource hosted by SciLifeLab Data Centre.

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 System (DDS)