Version 1

Workflow Type: Galaxy

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and excludes reads derived from such "tainted" amplicons when calculating allele-frequencies of other variants.


ID Name Description Type
ARTIC primer BED ARTIC primer BED BED file containing ARTIC primer positions. Can be retrieved from
  • File
ARTIC primers to amplicon assignments ARTIC primers to amplicon assignments Six column BED dataset used by ivar trim and ivar removereads for assigning primers to amplicons. Can be retrieved from
  • File
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
Paired Collection Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding
  • File[]


ID Name Description
4 fastp
5 Map with BWA-MEM
6 Samtools view
7 ivar trim
8 Samtools stats
9 Realign reads
10 Insert indel qualities
11 QualiMap BamQC
12 Call variants
13 Flatten Collection __FLATTEN__
14 Lofreq filter
15 MultiQC
16 ivar removereads
17 Call variants
18 VCF-VCFintersect:
19 Replace Text
20 VCF-VCFintersect:
21 Lofreq filter
22 SnpEff eff covid19 version


ID Name Description Type
fastp_html_report fastp_html_report n/a
  • File
fastp_reads_output fastp_reads_output n/a
  • File
mapped_reads 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
realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals n/a
  • File
bamqc_html_output bamqc_html_output n/a
  • File
bamqc_raw_output bamqc_raw_output n/a
  • File
preliminary_variants_1 preliminary_variants_1 n/a
  • File
bamqc_raw_output_flattened bamqc_raw_output_flattened n/a
  • File
filtered_preliminary_variants filtered_preliminary_variants n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
preprocessing_and_mapping_plots preprocessing_and_mapping_plots n/a
  • File
amplicon_removal_output amplicon_removal_output n/a
  • File
preliminary_variants_2 preliminary_variants_2 n/a
  • File
lost_variants_tmp lost_variants_tmp n/a
  • File
lost_variants lost_variants n/a
  • File
variants variants n/a
  • File
soft_filtered_variants soft_filtered_variants 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 0d8566b
help Creators and Submitter
Not specified
Additional credit

Wolfgang Maier


Views: 1154   Downloads: 152

Created: 1st Mar 2021 at 12:11

help Attributions


Total size: 108 KB
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