Science For Life Laboratory

Login: SciLifeLab

Company: null

Location: Stockholm

email: info@scilifelab.se

Blog: http://www.scilifelab.se

Members

  1. Denis Moreno
  2. Francesco
  3. Joel Gruselius
  4. Johan Dahlberg
  5. Johannes Alneberg
  6. Kenny Billiau
  7. Måns Magnusson
  8. Marcel Martin
  9. Martin Dahlö
  10. Matilda Åslin
  11. Mattias Ormestad
  12. Maxime Garcia
  13. Niclas Jareborg
  14. Per Kraulis
  15. Phil Ewels
  16. Pontus Larsson
  17. Remi-Andre Olsen
  18. Rickard Hammarén
  19. Robin Andeer
  20. Szilveszter Juhos
  21. null
  22. null
  23. null
  24. null
  25. null
  26. null
  27. null

Repositories

bcbb
Useful bioinformatics code, primarily in Python and R
bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysis
bcbio-nextgen-deploy
Suite of scripts to automatically deploy nextgen pipeline
blogs
A collection of blogs written by SciLifeLab affiliated authors
bravo-protocols
VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.
CAW
Cancer Analysis Workflow: a complete open source pipeline to detect somatic variants from WGS data
CAW
Cancer Analysis Workflow: a complete open source pipeline to detect somatic variants from WGS data
CAW-containers
Containers for CAW
cloudbiolinux
CloudBioLinux: automating resource preparation for biological analysis
cookiecutter
Template for your own top-end Nextflow pipeline, customised using Cookiecutter
courses
Course homepages for some of the courses given at SciLifeLab
dotfiles
null
external_kpis
null
facs
Fast and Accurate Classification of Sequences using Bloom filters
flowcell_parser
Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output
gapest
Reference implementation of the scaffolding gap size estimation algorithm by Kristoffer Sahlin
genologics
Python interface to the GenoLogics LIMS server via its REST API.
genologics_sql
Python interface for the Genologics Postgres database.
genomics-dashboard
null
genomics-status
Tornado server for tracking samples at NGI Stockholm
hugin
Status monitor
internal-provisioning
Ansible repository for deployment stuff
joint_variant_calling
null
LIMS2DB
null
miRNA_processing
Scripts to process miRNA from trimming through annotation.
modules.sf.net
Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)
NGI-CellRaiser
Pipeline for analysing 10X single cell data
NGI-ChIPseq
Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm
NGI-ExoSeq
(WIP) Nextflow Exome Sequencing Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure. https://ngisweden.scilifelab.se/
NGI-MethylSeq
Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
NGI-NeutronStar
De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.
NGI-NextflowDocs
Common documentation for National Genomics Infrastructure pipelines built with Nextflow
cookiecutter
Template for your own top-end Nextflow pipeline, customised using Cookiecutter
NGI-RNAfusion
Attempt at setting up a pipeline for fusion detection as an addon to the previously existing NGI-RNAseq pipeline.
NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
NGI-smRNAseq
Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
ngs.test.data
Test data set generation for ngs
NouGAT
NouGAT is a pipeline that automates de novo assembly project tasks, generating a first draft assembly.
opensource.scilifelab-theme
WordPress theme for Open Source SciLifeLab website.
portal
SciLifeLab Genomics Customer Portal
ratatosk
null
ratatosk.ext.scilife
Ratatosk extension for use at Science for Life Laboratory
CAW
Cancer Analysis Workflow: a complete open source pipeline to detect somatic variants from WGS data
CAW
Cancer Analysis Workflow: a complete open source pipeline to detect somatic variants from WGS data
Sarek-data
Sarek test data and references
scilifelab
Misc code snippets for Science For Life Laboratory
scilifelab_epps
A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
scilifelab.github.io
Web portal for open source (research) projects at SciLifeLab
scilifelab_parsers
Module for scilifelab parsers of metrics and other files
slog
simple lab logging system
Sarek-data
Sarek test data and references
software-development
General guidelines and style guide for software developed at SciLifeLab
specfiles
rpm specfiles used for building packages in use at SciLifeLab
standalone_scripts
Repository to store standalone scripts that do not belong to any bigger package or repository
statusdb
Python wrappers and methods to work with CouchDB's instance at NGI Stockholm
SVDB
structural variant database software
TACA
Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
TIDDIT
TIDDIT - structural variant calling
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.