Workflow Type: Galaxy

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 higher error rate than Illumina-sequenced reads and are therefor plagued more by false-positive variant calls, this workflow does make no attempt to handle amplicons affected by potential primer-binding site mutations.

Inputs

ID Name Description Type
ONT-sequenced reads ONT-sequenced reads ONT reads from ARTIC assay with fastqsanger encoding n/a
Minimum read length Minimum read length Discard reads that are shorter than this length n/a
Maximum read length Maximum read length Discard reads that are longer than this length n/a
NC_045512.2 FASTA sequence of SARS-CoV-2 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome n/a
ARTIC primer BED ARTIC primer BED n/a n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a
invcf invcf runtime parameter for tool Lofreq filter n/a
infile infile runtime parameter for tool Replace n/a

Steps

ID Name Description
0 ONT-sequenced reads ONT reads from ARTIC assay with fastqsanger encoding
1 Minimum read length Discard reads that are shorter than this length
2 Maximum read length Discard reads that are longer than this length
3 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
4 ARTIC primer BED
5 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
6 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
7 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
8 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1
9 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
10 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1
11 medaka consensus tool toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2
12 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
13 medaka variant tool toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy3
14 Flatten Collection __FLATTEN__
15 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
16 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
17 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
18 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3

Outputs

ID Name Description Type
out1 out1 n/a input
report_html report_html n/a html
alignment_output alignment_output n/a bam
outputsam outputsam n/a input
output_bam output_bam n/a bam
output output n/a tabular
output_bam output_bam n/a bam
out_result out_result n/a h5
raw_data raw_data n/a input
output_html output_html n/a html
out_result out_result n/a vcf
out_annotated out_annotated n/a vcf
out_log out_log n/a tabular
output output n/a input
snpeff_output snpeff_output n/a vcf
statsFile statsFile n/a html
stats stats n/a input
plots plots n/a input
html_report html_report n/a html
outvcf outvcf n/a vcf
outfile outfile n/a input
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 518   Downloads: 31

Created: 12th Mar 2021 at 13:41

Last updated: 27th Jul 2021 at 03:01

Last used: 19th Sep 2021 at 09:40

help Attributions

None

Version History

Version 3 (latest) Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.2.1

Version 2 Created 9th Apr 2021 at 03:00 by WorkflowHub Bot

Updated to v0.2

Version 1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot

No revision comments

Related items

Powered by
(v.1.12.0-master)
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH