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Swedish Pathogens Portal SciLifeLab

Tools catalogue

A collection of tools relevant to infectious disease research.

BIAFlows
BIAFlows
Open-source web platform to benchmark and reproducibly deploy bioimage analysis workflows.
Bioimage Informatics Search Engine (BISE)
Bioimage Informatics Search Engine (BISE)
Search engine for tools, training materials, and data in bioimage analysis.
BLAST
BLAST
The BLAST service uses BLAST (Basic Local Aligment Search Tool) to search against public or private genomes or other databases using DNA or protein sequence(s).
BRC Analytics
BRC Analytics
BRC Analytics provides access to curated genomic data for pathogens, hosts, and vectors using reference assemblies from NCBI Datasets, visualized through the UCSC Genome Browser, and supports user-uploaded sequencing data for integrated analyses. It offers browser-based analytical workflows powered by Galaxy and the Texas Advanced Computing Center (TACC), enabling analyses such as RNA-seq, genome annotation, comparative genomics, and other genomics workflows on scalable cloud computing resources.
Comparative Systems
Comparative Systems
The Comparative Systems Service allows users to identify a set of pathways, subsystems and protein families for given genome(s) or genome group(s).
Comprehensive Genome Analysis
Comprehensive Genome Analysis
The Comprehensive Genome Analysis Service provides a streamlined analysis "meta-service" that accepts raw reads and performs a comprehensive analysis including assembly, annotation, identification of nearest neighbours, a basic comparative analysis that includes a subsystem summary, phylogenetic tree, and the features that distinguish the genome from its nearest neighbours.
COVID-19 Data Repository on ICPSR
COVID-19 Data Repository on ICPSR
Repository of social, behavioral, and health sciences research data on COVID-19, hosted on ICPSR’s open platform.
COVID-19 Disease Map
COVID-19 Disease Map
Collaborative knowledgebase of molecular interaction diagrams of host–pathogen interactions specific to SARS-CoV-2, built from literature evidence.
COVID-19 Social Science Research Tracker
COVID-19 Social Science Research Tracker
A curated tracker of COVID-19 related social science research projects, datasets, and initiatives.
Differential Expression Import
Differential Expression Import
The Differential Expression Import Service facilitates upload of user-provided, pre-processed differential expression datasets generated by microarray, RNA-Seq, or proteomic technologies to the user's private workspace.
Fastq Utilites
Fastq Utilites
The Fastq Utilites Service provides capability for aligning, measuring base call quality, and trimmiing fastq read files.
Galaxy COVID-19 Analysis Portal
Galaxy COVID-19 Analysis Portal
Open-access platform providing curated workflows for SARS-CoV-2 analysis across genomics, cheminformatics, and proteomics. Enables variant tracking, docking, MS analyses, and real-time surveillance with mirrored datasets and training.
Genome Annotation
Genome Annotation
The Genome Annotation Service provides annotation of genomic features using the RAST tool kit (RASTtk) for bacteria and VIGOR4 for viruses. The service accepts a FASTA formatted contig file and an annotation recipe based on taxonomy to provide an annotated genome.
Genome Assembly
Genome Assembly
The Genome Assembly Service allows single or multiple assemblers to be invoked to compare results. The service attempts to select the best assembly.
Genomic Data Commons
Genomic Data Commons
The Genomic Data Commons (GDC) is a cancer knowledge network that supports hosting, standardisation, and analysis of genomic, clinical, and biospecimen data from cancer research programs. The GDC harmonises raw sequencing data, identifies and applies state-of-the-art bioinformatics methods for generating mutation calls, structural variants and other high-level data, and provides scalable downloads and web-based analysis tools.
HPA UMAP
HPA UMAP
ImJoy plugin to explore Human Protein Atlas single-cell UMAP projections interactively in the browser.
ID Mapper
ID Mapper
The ID Mapper tool maps PATRIC identifiers to those from other prominent external databases such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc. Alternatively, it can map a list of external database identifiers to the corresponding PATRIC features.
ImJoy
ImJoy
Plugin-powered hybrid computing platform for deploying deep learning applications, including advanced image analysis tools
ITK/VTK Viewer
ITK/VTK Viewer
Web-based viewer for visualising images using ITK/VTK pipelines; supports large multidimensional biomedical data.
Kaibu
Kaibu
Web application for visualization and annotation of multidimensional images, supporting layers, shapes, and interactive settings. Runs directly in the browser.
Metagenomic Binning
Metagenomic Binning
The Metagenomic Binning Service accepts either reads or contigs, and attempts to "bin" the data into a set of genomes. This service can be used to reconstruct bacterial and archael genomes from environmental samples.
Metagenomic Read Mapping
Metagenomic Read Mapping
The Metagenomic Read Mapping Service uses KMA to align reads against antibiotic resistance genes from CARD and virulence factors from VFDB.
mOTUS
mOTUS
The mOTUs (MG-based Operational Taxonomic Units) approach leverages well-established universal, single-copy, protein-coding marker genes to profile microbial abundances in shotgun metagenomic data.
National Library of Sweden – SweBERT models
National Library of Sweden – SweBERT models
Swedish BERT and ALBERT models for natural language processing, trained on large Swedish corpora.
Open Science Framework (OSF)
Open Science Framework (OSF)
As a collaboration tool, OSF helps research teams work on projects privately or make the entire project publicly accessible for broad dissemination. As a workflow system, OSF enables connections to the many products researchers already use, streamlining their process and increasing efficiency.
Phylogenetic Tree Builder
Phylogenetic Tree Builder
The Phylogenetic Tree Building Service enables construction of custom phylogenetic trees for user-selected genomes.
Proteome Comparison
Proteome Comparison
The Proteome Comparison Service performs protein sequence-based genome comparison using bidirectional BLASTP. This service allows users to select genomes and compare them to reference genome.
RNA-Seq Analysis
RNA-Seq Analysis
The RNA-Seq Analysis Service provides services for aligning, assembling, and testing differential expression on RNA-Seq data.
SARS-CoV-2 Genome Assembly and Annotation
SARS-CoV-2 Genome Assembly and Annotation
The SARS-CoV-2 Genome Assembly and Annotation Service provides a streamlined "meta-service" that accepts raw reads and performs genome assembly, annotation, and variation analysis.
scispaCy
scispaCy
Python package with spaCy models for efficient processing of biomedical and clinical text.
Similar Genome Finder
Similar Genome Finder
The Similar Genome Finder Service will find similar public genomes in PATRIC or compute genome distance estimation using Mash/MinHash. It returns a set of genomes matching the specified similarity criteria.
spaCy
spaCy
Industrial-strength NLP library integrating deep learning models for a wide range of text analysis tasks.
Sub-species classification tool
Sub-species classification tool
The sub-species classification tool assigns the genotype/subtype of a virus, based on the genotype/subtype assignments maintained by the International Committee on Taxonomy of Viruses (ICTV). This tool infers the genotype/subtype for a query sequence from its position within a reference tree. The service uses the pplacer tool with a reference tree and reference alignment and includes the query sequence as input. Interpretation of the pplacer result is handled by Cladinator.
Swedish Public Employment Service – SweBERT models
Swedish Public Employment Service – SweBERT models
Swedish BERT language models provided by the Swedish Public Employment Service for natural language processing research.
Tn-Seq Analysis
Tn-Seq Analysis
The Tn-Seq Analysis Service facilitates determination of essential and conditionally essential regions in bacterial genomes from data generated from transposon insertion sequencing (Tn-Seq) experiments.
Vizarr
Vizarr
Client-side browser tool for viewing Zarr-based images with Viv & ImJoy; embeddable into webpages for live visualisation.
Whole Genome Alignment
Whole Genome Alignment
The Whole Genome Alignment Service aligns genomes using progressiveMauve.
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