Swarm v3: towards tera-scale amplicon clustering
Aug. 16, 2021 2:43 PM
"The new version 3 of the Swarm software is a major step towards clustering extremely large amplicon datasets used in microbiome studies. It includes extensive improvements that make it about 10 times faster and twice as memory efficient as the previous version. Swarm makes it possible to cluster a huge dataset in reasonable time at one go, unlike other approaches where a large dataset needs to analysed in smaller portions," says Torbjørn Rognes, professor at the Centre for Bioinformatics.
A reference material for the genetic structure of Norway published
Aug. 11, 2021 8:49 AM
In a collaboration with deCODE Genetics, we were able to genotype a relatively representative cohort of the Norwegian population to generate a reference material for the genetic structure of Norway. “Somewhat surprisingly, no such study has previously characterized the genetic structure of Norway to any significant detail, and we are thrilled to provide this for future reference”, says professor Eivind Hovig. Among the novel findings is that historically there has been more limited genetic variation in the southern Norwegian counties of Agder, Telemark and Rogaland, indicating a level of genetic isolation.
Reporting the clinical impact of germline variants in human cancers
Aug. 10, 2021 11:41 AM
“Many human cancers are rooted in rare germline mutations, but identifying them and understanding their clinical impact is a considerable challenge. We have created a comprehensive bioinformatics workflow that successfully prioritizes cancer-predisposing DNA variants detected from high-throughput sequencing. Importantly, our reporting tool also highlights any variant with implications for prognosis or treatment options”, says Eivind Hovig, Professor and leader of the Centre for Bioinformatics.
The study, financed by the Norwegian Research Council, was recently published in the International Journal of Cancer and can be found here. The bioinformatics tool is named Cancer Predisposition Sequencing Reporter (CPSR), and was established in collaboration with researchers at Oslo University Hospital and researchers from the University of Melbourne in Australia.
Ten simple rules for quick and dirty scientific programming
June 16, 2021 10:48 AM
“We argue that a quick and dirty style of programming is not necessarily bad: the quicker you code, the more scientific ideas you can potentially test and publish. However, if coding quickly means coding sloppily, then bugs, false conclusions, and article retractions may be the result. Furthermore, if your code becomes increasingly complex and messy over time, then adapting it to new tasks will be difficult, potentially stalling your research progress” says Geir Kjetil Sandve, Professor at the Centre for Bioinformatics.
The study was recently published in the popular ten simple rules series of PLOS Computational Biology and can be found here.
The latest publications from the Centre
The Oslo Ischaemia Study: cohort profile
BMJ Open, 11 (10), e049111
Whole genome copy number analyses reveal a highly aberrant genome in TP53 mutant lung adenocarcinoma tumors
BMC Cancer, 21 (1), 1089
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq
PLoS One, 16 (10), e0258029
Software developed at the centre
Software for extraction of DNA copy number motifs in cancer
Chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Comparison of Adaptive Immune Receptor Repertoires
Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires
ScaR — a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors
Highly-scalable and high-resolution amplicon clustering
A versatile open source tool for metagenomics
ELIXIR Norway is the Norwegian national node of ELIXIR, the pan-European infrastructure for biological information, supporting life science research and its translation to medicine, environment, the bioindustries and society. This organization is a virtual organization where the Center of Bioinformatics hosts the regional Oslo node. It participates to the national help-desk user support, and in that activity also collaborates and coordinates closely with the Helse Sør-Øst-funded Bioinformatics Core facility.