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
report_html report_html n/a
alignment_output alignment_output n/a
outputsam outputsam n/a
output_bam output_bam n/a
output output n/a
output_bam output_bam n/a
out_result out_result n/a
raw_data raw_data n/a
output_html output_html n/a
out_result out_result n/a
out_annotated out_annotated n/a
out_log out_log n/a
output output n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
stats stats n/a
plots plots n/a
html_report html_report n/a
outvcf outvcf n/a
outfile outfile n/a
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 155   Downloads: 0

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:00

Last used: 23rd Oct 2021 at 12:18

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Version History

Version 1 (latest) Created 30th Aug 2021 at 17:00 by Simone Leo

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Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

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