COVID-19-ARTIC-ONT (v0.1)
Version 1

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 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
16 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
17 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
18 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19

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
soft_filtered_variants soft_filtered_variants n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
soft_filtered_variants_fixed soft_filtered_variants_fixed n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats n/a
  • File

Version History

Version 1 (earliest) Created 1st Mar 2021 at 12:11 by WorkflowHub Sandbox Bot

Added/updated 8 files


Open master 26abc4a
help Creators and Submitter
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Additional credit

Wolfgang Maier

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Views: 1080   Downloads: 117

Created: 1st Mar 2021 at 12:11

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