The current tools under development and maintenance by NBIS staff are listed below. For more detailed information on the tools, follow the links. See also the SciLifeLab Open Source website for tools developed at other SciLifeLab platforms.
AGAT
URL: https://github.com/NBISweden/AGAT
Another Gff Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
Software type: Command-line tool
Platform: Linux, Mac, Windows
Development status: Maintained
Released: Yes
Affiliation: nbis.se
ChIP-seq QC pipeline
URL: https://github.com/ewels/clusterflow
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 type: Workflow
Platform: Linux
Development status: Maintained
Released: Yes
Contact: jakub.westholm@scilifelab.se
Affiliation: nbis.se
EMBLmyGFF3
URL: https://github.com/NBISweden/EMBLmyGFF3
Publications: Norling, Jareborg & Dainat, 2018
Software to convert GFF3 and fasta to legal EMBL format suitable for the submission to the European Nucleotide Archive (ENA) database.
Software type: Command-line tool
Platform: Linux, Mac
Development status: Maintained
Released: Yes
Affiliation: nbis.se
GUESSmyLT
URL: https://github.com/NBISweden/GUESSmyLT
Publications: Berner Wik, Olin, Vigetun Haughey, Klasson & Dainat, 2019
Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.
Software type: Command-line tool
Platform: Linux, Mac, Windows
Development status: Maintained
Released: Yes
Affiliation: nbis.se
IgDiscover
URL: http://igdiscover.se/
Publications: Corcoran et al., 2016
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).
Software type: Command-line tool
Platform: Linux, Mac
Development status: Active
Released: Yes
Contact: http://igdiscover.se/
PI: Gunilla Karlsson Hedestam
Affiliation: ki.se
Metabolic Atlas
Publications: Wang et al., 2021 , Robinson et al., 2020
Metabolic Atlas integrates open source genome-scale metabolic models (GEMs) of human and yeast for easy browsing and analysis.
Software type: Database portal, Web application, Web API, Web service
Development status: Active
Released: Yes
Contact: contact@metabolicatlas.org
PI: Jens Nielsen
Affiliation: chalmers.se
MrBayes
URL: http://nbisweden.github.io/MrBayes/
Publications: Huelsenbeck & Ronquist, 2001
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.
Software type: Command-line tool
Platform: Linux, Windows, Mac
Development status: Maintained
Released: Yes
Contact: http://nbisweden.github.io/MrBayes/
PI: Fredrik Ronquist
Affiliation: nrm.se
PRECOG
URL: http://precog.lundberg.gu.se/
Publications: Fernandez-Ricaud et al., 2016
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.
Software type: Desktop application, Command-line tool, Web application
Platform: Windows
Development status: Maintained
Released: Yes
Contact: luciano.fernandez@marine.gu.se
PI: Anders Blomberg
Affiliation: gu.se
Proteios
URL: http://www.proteios.org
Publications: Garden et al., 2005
A multi-user platform for analysis and management of proteomics data.
Software type: Web application
Development status: Maintained
Released: Yes
Contact: http://ms-utils.org
PI: Fredrik Levander
Affiliation: immun.lth.se
Sarek
URL: https://nf-co.re/sarek
Publications: Garcia M al. 2020
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).
Software type: Command-line tool, Workflow
Platform: Linux
Development status: Active
Released: Yes
Contact: maxime.garcia@scilifelab.se
Affiliation: scilifelab.se
SweFreq
URL: https://swefreq.nbis.se
Publications: Ameur et al., 2017
Server hosting whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project.
Software type: Web application
Development status: Maintained
Released: Yes
Contact: swefreq@scilifelab.se
PI: Ulf Gyllensten
Affiliation: scilifelab.se
The Human Protein Atlas
URL: http://www.proteinatlas.org/
Publications: Uhlen et al., 2010 , Uhlen et al., 2015
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.
Software type: Database portal
Development status: Active
Released: Yes
Contact: contact@proteinatlas.org
PI: Mathias Uhlén
Affiliation: kth.se
Used in: Kampf et al., 2014 , Lindskog et al., 2015 , Edfors et al., 2016
Topcons
URL: https://topcons.net/
Publications: Tsirigos et al., 2015
Consensus prediction of membrane protein topology and signal peptides
Software type: Web application
Development status: Maintained
Released: Yes
Contact: http://bioinfo.se/
PI: Arne Elofsson
Affiliation: dbb.su.se
wgs-structvar
URL: https://github.com/NBISweden/wgs-structvar
Publications: Ameur et al., 2017
A workflow for standardized calling and filtering of structural variants, designed for whole genome sequencing projects.
Software type: Command-line tool
Platform: Linux
Development status: Maintained
Released: Yes
Contact: https://nbis.se
PI:
Affiliation: nbis.se
WhatsHap
URL: http://whatshap.readthedocs.io
Publications: Patterson et al., 2015 , Garg et al., 2016
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.
Software type: Command-line tool
Platform: Linux, Mac
Development status: Active
Released: Yes
Contact: https://lists.cwi.nl/mailman/listinfo/whatshap
PI: Tobias Marschall
Affiliation: mpi-inf.mpg.de
Xferticket
URL: https://xferticket.nbis.se
Service for facilitating transfer of big datasets to and from nbis experts.
Software type: Web application
Development status: Maintained
Released: Yes
Contact: cto@nbis.se
Affiliation: nbis.se
contigtax UNDER DEVELOPMENT
URL: https://github.com/NBISweden/contigtax
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.
Software type: Command-line tool
Platform: Linux, Mac
Development status: Active
Released: No
Contact: john.sundh@nbis.se
Affiliation: nbis.se
HaloPlex variant calling pipeline UNDER DEVELOPMENT
Publications: Tuominen et al., 2016 , Dalin et al., 2017
A pipeline for calling variants from targeted DNA sequencing data obtained using the HaloPlex method.
Software type: Workflow
Platform: Linux
Development status: Active
Released: No
Contact: par.engstrom@scilifelab.se
Affiliation: nbis.se
LocalEGA UNDER DEVELOPMENT
URL: https://github.com/NBISweden/LocalEGA
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.
Software type: Command-line tool, Workflow
Platform: Linux, Mac
Development status: Active
Released: No
Contact: ega@nbis.se
Affiliation: nbis.se
Single-cell RNA-seq analysis workflow UNDER DEVELOPMENT
URL: https://bitbucket.org/scilifelab-lts/lts-workflows-sm-scrnaseq/branch/develop
A workflow for quality control and basic analysis of single-cell RNA-seq data.
Software type: Workflow
Platform: Linux
Development status: Active
Released: No
Contact: asa.bjorklund@scilifelab.se
Affiliation: nbis.se