sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA

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, if possible, excludes 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 for amplicon bias correction #main/Minimum DP for 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
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
7 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
8 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
9 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
10 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
11 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
12 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
13 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy0
14 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
15 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
16 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
17 Flatten Collection __FLATTEN__
18 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy0
19 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
20 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
21 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
22 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
23 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
24 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
25 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
26 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
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_variants #main/lost_variants n/a
  • File
lost_variants_tmp #main/lost_variants_tmp 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_2 #main/preliminary_variants_2 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 #main/variants n/a
  • File
variants_fixed_header #main/variants_fixed_header 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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Wolfgang Maier

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Views: 825   Downloads: 9

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:00

Last used: 7th Dec 2022 at 02:18

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