Genomic Medicine Sweden

jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

pgx

Pharmacogenomics pipeline

gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

tomte

gms_16S

A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.

Information-specifications

poppy

Twist_Solid

Pipeline for Solid tumours

RareDisease_RNA_workflow

GMS-uploader

utility for uploading sequence and metadata to the NGP

raredisease

Call and score variants from WGS/WES of rare disease patients.

taxpasta

TAXnomic Profile Aggregation and STAndardisation

Twist_Solid_pipeline_files

Design and filter files used by the pipeline

NGPGlue

Small scripts and other similar NGP solutions of sensitive nature

configs

Config files used to define parameters specific to compute environments at different Institutions

docker-sc2reporter

Dockerized version of the sc2reporter program.

gmsmetapost

GMS Metagenomics post-classification

mag

Assembly and binning of metagenomes

meta-val

nf-core/taxprofiler post-processing; verification of classification results, consensus maps

meta-vis

Visualisation of metagenomic analysis results

microbiology

A repo to collect information about all different projects we have in GMS-Micro

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

nextflow-modules

Shared nextflow modules and assets

NGPIris

NGPIris 👁 (intelligence and repository interface software) is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform

sc2reporter

A web based analys tool for Sars-CoV-2 data

taxprofiler

Taxonomic profiling of shotgun metagenomic data

test-datasets

Test data to be used for automated testing with the nf-core pipelines

validate-meta