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
ARTIC primer BED ARTIC primer BED n/a
  • File
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[]

Steps

ID Name Description
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
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
primer_trimmed_filtered_mapped_reads primer_trimmed_filtered_mapped_reads n/a
  • File
mapped_reads_stats mapped_reads_stats n/a
  • File
realigned_primer_trimmed_filtered_mapped_reads realigned_primer_trimmed_filtered_mapped_reads n/a
  • File
medaka_consensus_data medaka_consensus_data n/a
  • File
bamqc_raw_output bamqc_raw_output n/a
  • File
bamqc_html_output bamqc_html_output n/a
  • File
medaka_variant_calls medaka_variant_calls n/a
  • File
bamqc_raw_output_flattened bamqc_raw_output_flattened n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
lofreq_filtered lofreq_filtered n/a
  • File
annotated_softfiltered_variants annotated_softfiltered_variants n/a
  • File

Version History

Version 2 (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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help Creators and Submitter
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Wolfgang Maier

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Views: 1362   Downloads: 178

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:00

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