Genomic Medicine Sweden

Sweden

Pinned Repositories

gms-artic
A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
Language:Nextflow8 2 286
gms_16S
A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
Language:Groovy4 11 150
Information-specifications
3 9 11
jasen
Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Language:Nextflow9 17 1929
nallo
Language:Nextflow6 6 1483
pgx
Pharmacogenomics pipeline
Language:HTML8 8 212
poppy
Language:Python3 10 172
RareDisease_RNA_workflow
Language:Nextflow2 9 105
tomte
Language:Nextflow9 8 103
Twist_Solid
Pipeline for Solid tumours
Language:Python3 6 277

Genomic Medicine Sweden's Repositories

genomic-medicine-sweden/jasen
Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Language:Nextflow9 17 1929
genomic-medicine-sweden/tomte
Language:Nextflow9 8 103
genomic-medicine-sweden/gms-artic
A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
Language:Nextflow8 2 286
genomic-medicine-sweden/pgx
Pharmacogenomics pipeline
Language:HTML8 8 212
genomic-medicine-sweden/nallo
Language:Nextflow6 6 1483
genomic-medicine-sweden/gms_16S
A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
Language:Groovy4 11 150
genomic-medicine-sweden/Information-specifications
3 9 11
genomic-medicine-sweden/poppy
Language:Python3 10 172
genomic-medicine-sweden/Twist_Solid
Pipeline for Solid tumours
Language:Python3 6 277
genomic-medicine-sweden/RareDisease_RNA_workflow
Language:Nextflow2 9 105
genomic-medicine-sweden/meta-val
nf-core/taxprofiler post-processing; verification of classification results; consensus maps
Language:Nextflow12
genomic-medicine-sweden/meta-vis
Visualisation of metagenomic analysis results
1 9 22
genomic-medicine-sweden/micro-site-data-sharing
This repo shares data between sites for the development of GMS-micro solutions.
1 12 02
genomic-medicine-sweden/raredisease
Call and score variants from WGS/WES of rare disease patients.
Language:Nextflow1 0 0
genomic-medicine-sweden/taxpasta
TAXnomic Profile Aggregation and STAndardisation
Language:Python1 0 00
genomic-medicine-sweden/Twist_Solid_pipeline_files
Design and filter files used by the pipeline
1 8 0
genomic-medicine-sweden/NGPGlue
Small scripts and other similar NGP solutions of sensitive nature
Language:Perl0 9 30
genomic-medicine-sweden/docker-sc2reporter
Dockerized version of the sc2reporter program.
Language:JavaScript3 971
genomic-medicine-sweden/GMS_RD_LR
GMS Best practises for long read analysis
genomic-medicine-sweden/gmsmetapost
GMS Metagenomics post-classification
Language:Nextflow8 481
genomic-medicine-sweden/microbiology
A repo to collect information about all different projects we have in GMS-Micro
genomic-medicine-sweden/MIMOSA
genomic-medicine-sweden/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Language:Nextflow0 0
genomic-medicine-sweden/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Language:Python0 0
genomic-medicine-sweden/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
Language:HTML0 0
genomic-medicine-sweden/nextflow-modules
Shared nextflow modules and assets
Language:Perl0 0
genomic-medicine-sweden/NGPIris
NGPIris 👁 (intelligence and repository interface software) is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform
Language:Python8 363
genomic-medicine-sweden/taxprofiler
Taxonomic profiling of shotgun metagenomic data
Language:Nextflow1 351
genomic-medicine-sweden/test-datasets
Test data to be used for automated testing with the nf-core pipelines
0 0
genomic-medicine-sweden/validate-meta
Language:Python2 01