Workflows

What is a Workflow?

164 Workflows visible to you, out of a total of 164

sars-cov-2-ont-artic-variant-calling/COVID-19-ARTIC-ONT

Intergalactic Workflow Commission (IWC)

Tests All failing

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

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Created: 12th Mar 2021 at 13:41, Last updated: 21st Dec 2021 at 03:01

sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE

Intergalactic Workflow Commission (IWC)

Tests Passing

COVID-19 sequence analysis on Illumina Amplicon PE data

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, ...

Type: Galaxy

Creator: Peter van Heusden

Submitter: WorkflowHub Bot

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Created: 31st Aug 2021 at 03:01, Last updated: 21st Dec 2021 at 03:01

sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA

Intergalactic Workflow Commission (IWC)

Tests All failing

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

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Created: 12th Mar 2021 at 13:41, Last updated: 21st Dec 2021 at 03:01

sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA

Intergalactic Workflow Commission (IWC)

Tests Passing

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

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Created: 12th Mar 2021 at 13:41, Last updated: 21st Dec 2021 at 03:01

Workflows

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COVID-19: variation analysis on ARTIC ONT data

COVID-19 sequence analysis on Illumina Amplicon PE data

COVID-19: variation analysis on WGS SE data

COVID-19: variation analysis on WGS PE data

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