Workflow Type: Galaxy

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic 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 amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by 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 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 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 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 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 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[]
Read removal maximum AF 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 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
fastp_html_report fastp_html_report n/a
  • File
fastp_json_report fastp_json_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
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
primer_trimmed_filtered_mapped_reads primer_trimmed_filtered_mapped_reads n/a
  • File
preliminary_variants_1 preliminary_variants_1 n/a
  • File
bamqc_raw_output bamqc_raw_output n/a
  • File
bamqc_html_output bamqc_html_output n/a
  • File
filtered_preliminary_variants filtered_preliminary_variants n/a
  • File
preliminary_variants_1_filtered preliminary_variants_1_filtered n/a
  • File
bamqc_raw_output_flattened bamqc_raw_output_flattened n/a
  • File
amplicon_removal_output amplicon_removal_output 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
preliminary_variants_2 preliminary_variants_2 n/a
  • File
variants_fixed_partial variants_fixed_partial n/a
  • File
preliminary_variants_2_filtered preliminary_variants_2_filtered n/a
  • File
lost_filter_passing_variants lost_filter_passing_variants n/a
  • File
variants_fixed variants_fixed n/a
  • File
variants_fixed_header variants_fixed_header n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats n/a
  • File
annotated_softfiltered_variants annotated_softfiltered_variants n/a
  • File

Version History

v0.5.2 (latest) Created 7th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.5.2


Frozen v0.5.2 4ecb475

v0.5.1 Created 12th Jan 2024 at 03:01 by WorkflowHub Bot

Updated to v0.5.1


Frozen v0.5.1 6f8294e

v0.5 Created 12th Feb 2022 at 03:00 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 6a3c0a3

v0.4.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.4.2


Open master c4d5139

v0.4.1 Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.4.1


Frozen master 6638bd0

v0.4 Created 19th Jun 2021 at 03:00 by WorkflowHub Bot

Updated to v0.4


Frozen master 7836685

v0.3 Created 6th Jun 2021 at 03:00 by WorkflowHub Bot

Updated to v0.3


Frozen master 9c97358

v0.2 Created 9th Apr 2021 at 03:00 by WorkflowHub Bot

Updated to v0.2


Frozen master b89fc19

v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot

Added/updated 8 files


Frozen master 865c5cb
help Creators and Submitter
Creator
Submitter
License
Activity

Views: 10621

Created: 12th Mar 2021 at 13:41

Last updated: 28th Mar 2024 at 17:27

help Attributions

None

Total size: 93.9 KB
Powered by
(v.1.14.1)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH