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
Maximum read length Maximum read length Discard reads that are longer than this length
  • int?
Minimum read length Minimum read length Discard reads that are shorter than this length
  • int?
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
  • File
ONT-sequenced reads ONT-sequenced reads ONT reads from ARTIC assay with fastqsanger encoding
  • File[]
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.
  • File

Steps

ID Name Description
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
length_filtered_reads length_filtered_reads n/a
  • File
fastp_report fastp_report n/a
  • File
minimap2_mapped_reads minimap2_mapped_reads n/a
  • File
filtered_mapped_reads filtered_mapped_reads n/a
  • File
mapped_reads_stats mapped_reads_stats n/a
  • File
realigned_filtered_mapped_reads realigned_filtered_mapped_reads n/a
  • File
primer_trimmed_realigned_filtered_mapped_reads primer_trimmed_realigned_filtered_mapped_reads n/a
  • File
bamqc_raw_output bamqc_raw_output n/a
  • File
bamqc_html_output bamqc_html_output n/a
  • File
medaka_consensus_data medaka_consensus_data n/a
  • File
medaka_variants_general medaka_variants_general n/a
  • File
medaka_variants_pbs medaka_variants_pbs n/a
  • File
bamqc_raw_output_flattened bamqc_raw_output_flattened n/a
  • File
variants_pbs variants_pbs n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
variants_combined variants_combined n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats n/a
  • File
lofreq_filtered lofreq_filtered n/a
  • File
annotated_softfiltered_variants annotated_softfiltered_variants n/a
  • File

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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Additional credit

Wolfgang Maier

Submitter
License
Activity

Views: 3851   Downloads: 70

Created: 12th Mar 2021 at 13:41

Last updated: 21st Dec 2021 at 03:01

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