Tools

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.

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
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
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
Pcons
URL: http://pcons.net/
Publications: Wallner et al., 2007
Protein structure prediction meta server.
Software type: Web application
Development status: Maintained
Released: Yes
Contact: bjorn@sbc.su.se
PI: Arne Elofsson
Affiliation: sbc.su.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: http://opensource.scilifelab.se/projects/sarek/
Complete open source pipeline to detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data. 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
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
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
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
Metabolic Atlas v2 UNDER DEVELOPMENT
Publications: Pornputtapong et al., 2015
The Metabolic Atlas is a web resource for yeast and human metabolism visualising, and analysing, hundreds of different manually curated genome-scale metabolic models (GEMs) for different conditions.
Software type: Database portal, Web application, Web API, Web service
Development status: Active
Released: No
Contact: admin@metabolicatlas.org
PI: Jens Nielsen
Affiliation: chalmers.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