Bioinformatics Long-term Support (WABI)

National facility

SciLifeLab offers bioinformatics long-term support in the format of “embedded bioinformaticians”, senior bioinformaticians working in your project for an extended time, typically 6 – 12 calendar months. This support has been enabled by a generous grant from the Knut and Alice Wallenberg Foundation and is predominantly targeting projects that have generated high-throughput data of kinds that can be produced at the SciLifeLab platforms. The facility has state-of the art competence and technical know-how in large-scale sequence data analysis, including transcriptomics, variant detection and de novo genome assembly. Research groups interested in long-term bioinformatics support will have to send in a specific application, please see information in the right side bar.

SERVICES

  • All NGS applications. Virtually all kinds of sequencing projects are supported, as well as projects combining sequencing data with data from other SciLifeLab platforms.
  • Free of charge. Projects are reviewed by a national committee and selected based on scientific level.
  • Long-term support. Senior bioinformaticians working in your project for a period of 6-12 months.

APPLICATIONS

Examples of technical areas of support:

  • Variant calling in model and non-model organisms
  • Human exome and whole-genome resequencing
  • Differential and allele-specific expression
  • De novo genome assembly
  • Metagenomics
  • Single-cell analyses
  • Integrative analyses of multiple types of "omics" data

EQUIPMENT

This facility only provides time as a resource. Computer equipment is provided mainly through SNIC.

RECENT PROJECTS

  • Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.  Kee et al. Cell Stem Cell (2017)
  • Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Corcoran et al. Nature Communications (2016)
  • Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Ståhl et al. Science (2016).
  • RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. Le Rhun et al. RNA Biology (2016).
  • The human gut microbiome as a transporter of antibiotic resistance genes between continents. Bengtsson-Palme et al. Antimicrobial Agents and Chemotherapy (2015).
  • Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Steige et al. Molecular Biology and Evolution (2015).
  • The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. Lindqvist et al. Human Mutation (2015).
  • The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Poelstra et al. Science (2014).

A full publication list is provided at the Long-term Bioinformatics Support wiki.