Workflow Type: Galaxy

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 tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.

Inputs

ID Name Description Type
ARTIC primer BED #main/ARTIC primer BED BED file containing ARTIC primer positions. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
  • File
ARTIC primers to amplicon assignments #main/ARTIC primers to amplicon assignments Used by ivar trim and ivar removereads for assigning primers to amplicons. Should have one line of tab-separated primer names per amplicon. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
  • File
Minimum DP required after amplicon bias correction #main/Minimum DP required after amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of coverage of the site retains at least this value after amplicon removal.
  • int
Minimum DP_ALT required after amplicon bias correction #main/Minimum DP_ALT required after amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of variant-supporting reads at the site retains at least this value after amplicon removal.
  • int
NC_045512.2 FASTA sequence of SARS-CoV-2 #main/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 #main/Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding
  • array containing
    • File
Read removal maximum AF #main/Read removal maximum AF Maximum allele-frequency allowed for a primer binding site mutation to trigger amplicon removal. Variants with AF values above this threshold are treated as fixed variants, which won't generate amplicon bias.
  • float
Read removal minimum AF #main/Read removal minimum AF Minimum allele-frequency required for a candidate primer binding site mutation to trigger amplicon removal. Variants with AF values below this threshold are treated as possible false-positives, which are not worth the coverage loss associated with amplicon removal.
  • float

Steps

ID Name Description
8 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
10 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
11 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
12 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
13 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
14 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
15 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2
16 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
17 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
18 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
19 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
20 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
21 Filter failed datasets __FILTER_FAILED_DATASETS__
22 Flatten Collection __FLATTEN__
23 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy2
24 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
25 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
26 bcftools annotate toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
27 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
28 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
29 bcftools annotate toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
30 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
31 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
32 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0

Outputs

ID Name Description Type
amplicon_removal_output #main/amplicon_removal_output n/a
  • File
annotated_softfiltered_variants #main/annotated_softfiltered_variants n/a
  • File
annotated_variants #main/annotated_variants n/a
  • File
annotated_variants_stats #main/annotated_variants_stats n/a
  • File
bamqc_html_output #main/bamqc_html_output n/a
  • File
bamqc_raw_output #main/bamqc_raw_output n/a
  • File
bamqc_raw_output_flattened #main/bamqc_raw_output_flattened n/a
  • File
fastp_html_report #main/fastp_html_report n/a
  • File
fastp_json_report #main/fastp_json_report n/a
  • File
fastp_reads_output #main/fastp_reads_output n/a
  • File
filtered_mapped_reads #main/filtered_mapped_reads n/a
  • File
filtered_preliminary_variants #main/filtered_preliminary_variants n/a
  • File
lost_filter_passing_variants #main/lost_filter_passing_variants n/a
  • File
mapped_reads #main/mapped_reads n/a
  • File
mapped_reads_stats #main/mapped_reads_stats n/a
  • File
preliminary_variants_1 #main/preliminary_variants_1 n/a
  • File
preliminary_variants_1_filtered #main/preliminary_variants_1_filtered n/a
  • File
preliminary_variants_2 #main/preliminary_variants_2 n/a
  • File
preliminary_variants_2_filtered #main/preliminary_variants_2_filtered n/a
  • File
preprocessing_and_mapping_plots #main/preprocessing_and_mapping_plots n/a
  • File
preprocessing_and_mapping_reports #main/preprocessing_and_mapping_reports n/a
  • File
primer_trimmed_filtered_mapped_reads #main/primer_trimmed_filtered_mapped_reads n/a
  • File
realigned_primer_trimmed_filtered_mapped_reads #main/realigned_primer_trimmed_filtered_mapped_reads n/a
  • File
realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals #main/realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals n/a
  • File
variants_fixed #main/variants_fixed n/a
  • File
variants_fixed_header #main/variants_fixed_header n/a
  • File
variants_fixed_partial #main/variants_fixed_partial n/a
  • File

Version History

v0.5.3 (latest) Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

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