Tools

Another Gff Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.

Pipeline for quality control of ChIP-seq data, implemented as a plug-in for the workflow manager ClusterFlow. See pipelines/chipseq_qc.config in the ClusterFlow repository on GitHub.

Software to convert GFF3 and fasta to legal EMBL format suitable for the submission to the European Nucleotide Archive (ENA) database.

Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.

IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).

Metabolic Atlas integrates open source genome-scale metabolic models (GEMs) of human and yeast for easy browsing and analysis.

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

PRECOG is a tool developed to automate visualization, analysis and exploration of complex and highly resolved microbial growth data, as well as standardized extraction of the fitness components it contains. We hope that this tool will promote simplicity, transparency and standardization in microbial growth phenomics, and provide a portal with the standalone software and online tools so that other microbiology labs can easily upload, assess and visualize their growth data.

A multi-user platform for analysis and management of proteomics data.

Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. Previously known as Cancer Analysis Workflow (CAW).

Server hosting whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project.

Database with millions of high-resolution images. Expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images.

Consensus prediction of membrane protein topology and signal peptides

A workflow for standardized calling and filtering of structural variants, designed for whole genome sequencing projects.

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

Service for facilitating transfer of big datasets to and from nbis experts.

contigtax assigns taxonomy to contigs in metagenomic assemblies using sequence alignments against protein databases (e.g. UniRef) and calculation of lowest common ancestor in the taxonomic hierarchy.

A pipeline for calling variants from targeted DNA sequencing data obtained using the HaloPlex method.

The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. Local EGA handles data that are supposed to stay in Sweden.

A workflow for quality control and basic analysis of single-cell RNA-seq data.