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).
gmsmetapost
GMS Metagenomics post-classification
hydra-genetics_snv_indels
Collection of rules used to call snv and small indels.
JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core-sarek
raredisease
Call and score variants from WGS/WES of rare disease patients.
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
var-genes-ro
Virulence and Antibiotic Resistance Genes used with JASEN pipeline at the university hospital of Linköping, Sweden.
Genomic Medicine Linköping's Repositories
Genomic-Medicine-Linkoping/var-genes-ro
Virulence and Antibiotic Resistance Genes used with JASEN pipeline at the university hospital of Linköping, Sweden.
Genomic-Medicine-Linkoping/cnv_sv
Collection of rules used to call structural variants
Genomic-Medicine-Linkoping/gms-artic
A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
Genomic-Medicine-Linkoping/gmsmetapost
GMS Metagenomics post-classification
Genomic-Medicine-Linkoping/hydra-genetics_alignment
Snakemake module containing processing steps that should be performed during sequence alignment.
Genomic-Medicine-Linkoping/hydra-genetics_snv_indels
Collection of rules used to call snv and small indels.
Genomic-Medicine-Linkoping/JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Genomic-Medicine-Linkoping/LiSC
scRNA-seq
Genomic-Medicine-Linkoping/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Genomic-Medicine-Linkoping/nextflow_rnaseqfus
Genomic-Medicine-Linkoping/nf-core-sarek
Genomic-Medicine-Linkoping/pgx
Pharmacogenomics pipeline
Genomic-Medicine-Linkoping/qiaseq_qc
Pipeline based on hydra modules for in-house validation of qiagen's qiaseq bioinformatics pipeline
Genomic-Medicine-Linkoping/raredisease
Call and score variants from WGS/WES of rare disease patients.
Genomic-Medicine-Linkoping/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
Genomic-Medicine-Linkoping/STARlight
RNA-seq STAR Pipeline
Genomic-Medicine-Linkoping/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
Genomic-Medicine-Linkoping/TNscope
Sentieon TNscope basic pipeline
Genomic-Medicine-Linkoping/bioconda-recipes
Conda recipes for the bioconda channel.
Genomic-Medicine-Linkoping/hydra-genetics_prealignment
Snakemake module containing processing steps that should be performed before sequence alignment.
Genomic-Medicine-Linkoping/hydra-genetics_qc
Collection of rules performing QC and generating reports.
Genomic-Medicine-Linkoping/KITM_fastq_preprocessing
QC and trimming of fastq reads
Genomic-Medicine-Linkoping/nextstrain-auspice
Genomic-Medicine-Linkoping/parabricks
Snakemake module containing different analyses provided by parabricks.
Genomic-Medicine-Linkoping/pgx_module
Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.
Genomic-Medicine-Linkoping/snake_rnaseq
STAR pipeline
Genomic-Medicine-Linkoping/test-datasets
Test data to be used for automated testing with the nf-core pipelines
Genomic-Medicine-Linkoping/Twist_DNA
Genomic-Medicine-Linkoping/Twist_RNA
Genomic-Medicine-Linkoping/Twist_Solid
Pipeline for Solid tumours