Science For Life Laboratory

Sarek

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

TIDDIT

TIDDIT - structural variant calling

NGI-RNAseq

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

genologics

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

courses

Course homepages for some of the courses given at SciLifeLab

facs

Fast and Accurate Classification of Sequences using Bloom filters

TACA

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

genomics-status

Tornado server for tracking samples at NGI Stockholm

NGI-ExoSeq

This pipeline has moved! Please see:

flowcell_parser

Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

NGI-ChIPseq

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

umi-transfer

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

NGI-smRNAseq

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

scilifelab

Misc code snippets for Science For Life Laboratory

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

NGI-RNAfusion

RNA pipeline for fusion detection

standalone_scripts

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

internal-provisioning

Ansible repository for deployment stuff

Sarek-data

Sarek test data and references

taca-ngi-pipeline

A TACA plugin adding functionality relevant for the ngi_pipeline

NGI-NeutronStar

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

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

SVDB

structural variant database software

genologics_sql

Python interface for the Genologics Postgres database.

LIMS2DB

OrderPortal

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

bravo-protocols

VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

coronastatus

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

percolator

Semi-supervised learning for peptide identification from shotgun proteomics datasets

standalone_scripts-1

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