Bioinformatics Compute and Storage (UPPNEX)

National facility

The Bioinformatics compute and storage facility provides high-performance computing and storage resources, maintain relevant bioinformatics software and data (e.g. reference genomes), and offer associated user support. The facility is hosted at Uppsala Multidisciplinary Center for Advanced Computational Science (SNIC-UPPMAX), which is Uppsala University’s resource for high-performance computing and related know-how. Its reference group makes strategic and policy decisions, while a manager is responsible for daily operations.


  • Bioinformatics software. Maintenance of an extensive suite of bioinformatics software applications. Assistance with installation and updates
  • Computing and storage. High-performance computing and large-scale storage for bioinformatics, primarily for the Next Generation Sequencing (NGS) community in Sweden
  • Hardware and system administration. Expert management of high-performance computational hardware
  • Reference data. Maintenance of reference genomes and other shared data sources
  • Training services. Participates in various SciLifeLab workshops and courses, such as “Computational Methods for Massively Parallel Sequencing”. Provides computational resources for several other courses
  • User support. Provides technical user support for high-performance computing and NGS analyses on UPPNEX systems. Participates in the national bioinformatics support forum


  • Next-generation sequencing data analysis and management
  • Large-scale storage and archiving of image data
  • Management and analysis of drug screening data


  • Access to SweStore National Storage. Mainly for archiving data for longer periods of time.
  • Alignment programs. E.g. BWA, Mosaik, Bowtie, Tophat, MAQ, Bioscope and Lifescope
  • Backup system. Each project has a file area that every night is backed up on magnetic tapes in Linköping
  • Computational resources. Computer cluster with 2 000 000 computing hours per month
  • De novo assembly software. E.g. Abyss, Velvet and Mira
  • Downstream analysis programs. E.g. Cufflinks, MrBayes, SAM-tools, and Annovar
  • General software tools. E.g. BioPerl, Picard and GATK
  • High-bandwidth network. Fast connection to Swedish University Network (SUNET) backbone
  • High-memory computer. Large memory SMP with 2 TB RAM
  • Storage resources. Storage resources of 7 PB


Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O. Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. Gigascience. 2013 Jun 25;2(1):9. doi: 10.1186/2047-217X-2-9.


Mayrhofer M, Dilorenzo S, Isaksson A. Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue. Genome Biol. 2013 Mar 25;14(3):R24. doi:10.1186/gb-2013-14-3-r24.


Nystedt B et al.The Norway spruce genome sequence and conifer genome evolution. Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211.


Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013 Mar 21;495(7441):360-4. doi: 10.1038/nature11837.


Ellegren H et al.. The genomic landscape of species divergence in Ficedula flycatchers. Nature. 2012 Nov 29;491(7426):756-60. doi: 10.1038/nature11584.