@SciLifeLab

Science For Life Laboratory

Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research

Pinned repositories

  1. Sarek

    Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

    Nextflow 70 41

  2. NGI-RNAseq

    Forked from ewels/nf-core-rnaseq

    Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

    Groovy 44 40

  3. NGI-NeutronStar

    Forked from remiolsen/NGI-NeutronStar

    De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.

    Nextflow 1 1

  4. genologics

    Forked from pekrau/genologics

    Python interface to the GenoLogics LIMS server via its REST API.

    Python 22 36

  5. TACA

    Forked from guillermo-carrasco/TACA

    Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm

    Python 10 12

  6. NouGAT

    Forked from vezzi/NouGAT

    NouGAT is a pipeline that automates de novo assembly project tasks, generating a first draft assembly.

    Python 5 7

  • Repository to store standalone scripts that do not belong to any bigger package or repository

    Python 3 19 MIT Updated Sep 21, 2018
  • Tornado server for tracking samples at NGI Stockholm

    JavaScript 7 17 MIT Updated Sep 21, 2018
  • Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

    Nextflow 70 41 MIT Updated Sep 21, 2018
  • Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm

    Python 10 14 MIT 1 issue needs help Updated Sep 18, 2018
  • Python 1 6 MIT Updated Sep 17, 2018
  • RNA pipeline for fusion detection

    Groovy 2 5 MIT Updated Sep 17, 2018
  • TIDDIT - structural variant calling

    C++ 8 3 Updated Sep 17, 2018
  • Course homepages for some of the courses given at SciLifeLab

    HTML 14 62 Updated Sep 12, 2018
  • Sarek test data and references

    Python 1 3 MIT Updated Sep 10, 2018
  • A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

    Python 2 7 Updated Sep 5, 2018
  • NGI-ChIPseq Archived

    Forked from chuan-wang/NGI-ChIPseq

    Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm

    Groovy 5 33 MIT Updated Aug 20, 2018
  • NGI-RNAseq Archived

    Forked from ewels/nf-core-rnaseq

    Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

    Groovy 44 70 MIT 1 issue needs help Updated Aug 20, 2018
  • Python interface to the GenoLogics LIMS server via its REST API.

    Python 22 43 MIT Updated Aug 16, 2018
  • Python interface for the Genologics Postgres database.

    Python 1 7 MIT Updated Jul 20, 2018
  • NGI-smRNAseq Archived

    Forked from Hammarn/NGI-smRNAseq

    Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

    Groovy 4 19 MIT Updated Jul 12, 2018
  • Ansible repository for deployment stuff

    Python 2 4 Updated Jun 1, 2018
  • A TACA plugin adding functionality relevant for the ngi_pipeline

    Python 2 9 MIT Updated Apr 24, 2018
  • NGI-ExoSeq Archived

    Forked from senthil10/NGI-ExoSeq

    This pipeline has moved! Please see:

    Groovy 9 14 MIT Updated Apr 18, 2018
  • NouGAT

    Forked from vezzi/NouGAT

    NouGAT is a pipeline that automates de novo assembly project tasks, generating a first draft assembly.

    Python 5 14 MIT Updated Apr 10, 2018
  • Common documentation for National Genomics Infrastructure pipelines built with Nextflow

    Groovy 5 4 MIT Updated Mar 29, 2018
  • De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.

    Nextflow 1 2 MIT Updated Mar 22, 2018
  • NGI-MethylSeq Archived

    This pipeline has moved! Please see:

    Groovy 12 26 MIT Updated Mar 12, 2018
  • Misc code snippets for Science For Life Laboratory

    Python 6 25 MIT Updated Mar 8, 2018
  • Pipeline for analysing 10X single cell data

    Groovy 7 5 MIT Updated Jan 23, 2018
  • Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

    Python 5 12 MIT Updated Jan 10, 2018
  • VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

    Prolog 5 Apache-2.0 Updated Dec 18, 2017
  • CAW-containers Archived

    Containers for CAW

    4 2 Updated Nov 20, 2017
  • Shell 2 Updated Mar 15, 2017
  • Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

    Python 2 6 MIT Updated Oct 19, 2016
  • SVDB

    Forked from J35P312/SVDB

    structural variant database software

    Python 1 3 Updated Sep 27, 2016