GMS-Artic

A nextflow pipeline with a GMS touch for running the ARTIC network’s fieldbioinformatics tools

Jyotirmoy Das

Sofia Stamouli

Henning Onsbring

Tanja Normark

Isak Sylvin

Why it requires?

analyse whole genome sequence data from SARS-CoV-2.

requires pangolin typing information.

requires a semi/automated workflow (NextFlow).

development of production level, clinical data analysis tool

container-packed (Conda, Docker, Singularity) reproducible package

What it does?

Architecture of GMS-Artic

GitHub page

Major updates-v2.0.0

Docker container separated for Pangolin typing
- Illumina container: gms-artic-illumina
- Nanopore container: gms-artic-nanopore
- Pangolin container: gms-artic-pangolin - bi-weekly updated with GitHub action
Added separate package version files for each workflow
- versions: for Illumina and Nanopore
- pangoversion: for pangolin typing
- extra features for Illumina, flagstat, depth, VEP annotation
Illumina results works for sc2reporter visualization
additional QC features for Nanopore: fastqc, multiqc, pycoQC

  nextflow run main.nf 
      -profile singularity \
      --illumina \
      --prefix "test_illumina" \
      --directory .github/data/fastqs/ \
      --outdir illumina_test

  nextflow run main.nf \
      -profile singularity \
      --nanopolish \
      --prefix "test_nanopore_nanopolish" \
      --basecalled_fastq /fastq_pass/ \
      --fast5_pass /fast5_pass/ \
      --sequencing_summary sequencing_summary_FAK72834_298b7829.txt \
      --outdir nanopore_nanopolish

  nextflow run main.nf 
      -profile singularity \
      --medaka 
      --prefix "test_nanopore_medaka" \
      --basecalled_fastq /fastq_pass/ \
      --outdir nanopore_medaka

Pipeline processes

Illumina processes	Nanopore medaka processes	Nanopore nanopolish processes
articDownloadScheme	articDownloadScheme	articDownloadScheme
indexReference	-	-
versions	versions	versions
pangoversions	pangoversions	pangoversions
fastqc	fastqcNanopore	fastqcNanopore
-	-	pycoqc
readTrimming	articRemoveUnmappedReads	articRemoveUnmappedReads
-	articGuppyPlex	articGuppyPlex
-	articMinIONMedaka	articMinIONNanopolish
readMapping	-	-
flagStat	-	-
trimPrimerSequences	-	-
depth	-	-
callConsensusFreebayes	-	-
annotationVEP	-	-
callVariants	-	-
makeConsensus	-	-
makeQCCSV	makeQCCSV	makeQCCSV
writeQCSummaryCSV	writeQCSummaryCSV	writeQCSummaryCSV
statsCoverage	-	-
statsInsert	-	-
statsAlignment	-	-
multiqc	multiqcNanopore	multiqcNanopore
collateSamples	collateSamples	collateSamples
pangolinTyping	pangolinTyping	pangolinTyping
nextclade	nextclade	nextclade
getVariantDefinitions	getVariantDefinitions	getVariantDefinitions
makeReport	makeReport	makeReport

Let’s have a quick one minute demo

How the results look?

example: Output of Illumina workflow run

Interactive Result

Where to run?

NGP-server @ Gothenburg University
- SGE cluster
- supports MPI

Local run?

local-server
- Singularity/Conda, Nextflow installation
- AMD64 OS arch (only AMD64 supported container)

Acknowledgements

Genomic Medicine, Sweden
Clinical Genomics:
- Gothenburg
- Linköping
- Lund
- Örebro
- Stockholm
- Umeå
- Uppsala
all USERS of the pipeline!

Find us @ https://github.com/genomic-medicine-sweden/gms-artic
@ slack channel: genomicmedicinesweden.slack.com