Science For Life Laboratory

Science For Life Laboratory's repositories

Sarek

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

Language:NextflowMIT133 19 324

TIDDIT

TIDDIT - structural variant calling

Language:CythonNOASSERTION73 18 40

NGI-RNAseq

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

Language:GroovyMIT51 24 63

genologics

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

Language:PythonMIT29 29 38

courses

Course homepages for some of the courses given at SciLifeLab

Language:HTML21 230

facs

Fast and Accurate Classification of Sequences using Bloom filters

Language:Jupyter NotebookNOASSERTION16 20 55

NGI-MethylSeq

This pipeline has moved! Please see:

Language:GroovyMIT11 21 6

NGI-CellRaiser

Pipeline for analysing 10X single cell data

Language:GroovyMIT8 10 3

NGI-ExoSeq

This pipeline has moved! Please see:

Language:GroovyMIT8 10 17

NGI-ChIPseq

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

Language:GroovyMIT7 9 14

NGI-NextflowDocs

Common documentation for National Genomics Infrastructure pipelines built with Nextflow

Language:GroovyMIT5 20 1

NGI-smRNAseq

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

Language:GroovyMIT5 17 8

NouGAT

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

Language:PythonMIT5 24 7

scilifelab

Misc code snippets for Science For Life Laboratory

Language:PythonMIT5 24 68

umi-transfer

A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.

Language:RustMIT5 5 1

NGI-RNAfusion

RNA pipeline for fusion detection

Language:GroovyMIT4 17 4

CAW-containers

Containers for CAW

300

genomics-dashboard

Language:JavaScriptMIT300

Sarek-data

Sarek test data and references

Language:PythonMIT3 170

hugin

Status monitor

Language:Python200

NGI-NeutronStar

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

Language:NextflowMIT2 16 1

SVDB

structural variant database software

Language:Python2 80

genologics_sql

Python interface for the Genologics Postgres database.

Language:PythonMIT1 130

OrderPortal

A portal for orders (a.k.a. requests, project applications) to a SciLifeLab facility from its users.

Language:PythonMIT1 90

scilifelab_parsers

Module for scilifelab parsers of metrics and other files

Language:Python100

coronastatus

Open source webapp that let people report their health status to get overview of COVID-19 🇳🇴🇳🇱🇸🇰🇲🇽🇮🇹🇮🇳🇵🇭🇸🇪🇩🇰🇹🇷🇧🇪

Language:HTMLMIT02 4

external_kpis

Language:JavaScript000

joint_variant_calling

Language:Shell000

percolator

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Language:C++NOASSERTION020

standalone_scripts-1

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

Language:PythonMIT020