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
Primer binding sites info in BED format Primer binding sites info in BED format BED file containing (ARTIC) primer positions. For ARTIC primer schemes the file can be obtained from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources. n/a
input_file input_file runtime parameter for tool bcftools annotate n/a
sec_annotate sec_annotate runtime parameter for tool bcftools annotate n/a
sec_restrict sec_restrict runtime parameter for tool bcftools annotate n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: 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 Primer binding sites info in BED format BED file containing (ARTIC) primer positions. For ARTIC primer schemes the file can be obtained from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources.
5 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
6 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
7 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
8 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
9 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
10 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
11 Parse parameter value param_value_from_file
12 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
13 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1
14 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2
15 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
16 medaka consensus tool toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2
17 Filter failed __FILTER_FAILED_DATASETS__
18 medaka variant tool toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.3.2+galaxy1
19 medaka variant tool toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.3.2+galaxy1
20 Flatten Collection __FLATTEN__
21 bedtools Intersect intervals toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0
22 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
23 bcftools annotate toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
24 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
25 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
26 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
out_file1 out_file1 n/a
outfile outfile n/a
alignment_output alignment_output n/a
out_file out_file n/a
outputsam outputsam n/a
integer_param integer_param n/a
output output n/a
output_bam output_bam n/a
output_bam output_bam n/a
raw_data raw_data n/a
output_html output_html n/a
out_result out_result n/a
output output n/a
out_variants out_variants n/a
out_variants out_variants n/a
output output n/a
output output n/a
stats stats n/a
plots plots n/a
html_report html_report n/a
output_file output_file n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
outvcf outvcf n/a
outfile outfile n/a

Version History

v0.3.1 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.3.1


Open master 4948641

v0.3 Created 27th Oct 2021 at 15:45 by WorkflowHub Bot

Updated to v0.3


Frozen master 7d4b2aa

v0.2.1 Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.2.1


Frozen master ae0a424

v0.2 Created 9th Apr 2021 at 03:00 by WorkflowHub Bot

Updated to v0.2


Frozen master 7ce2e0e

v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot

Added/updated 8 files


Frozen master 3b99025
help Creators and Submitter
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Wolfgang Maier

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Views: 2366   Downloads: 60

Created: 12th Mar 2021 at 13:41

Last updated: 21st Dec 2021 at 03:01

Last used: 25th Jun 2022 at 17:01

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