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.

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 Six column BED dataset used by ivar trim and ivar removereads for assigning primers to amplicons. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
  • 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[]

Steps

ID Name Description
4 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
5 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
6 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
7 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1
8 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
11 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
12 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
13 Flatten Collection __FLATTEN__
14 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
15 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
16 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1
17 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
18 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
19 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
20 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
21 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
22 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
23 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_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
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

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

Updated to v0.5.3


Frozen v0.5.3 26a4baa

v0.5.2 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

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Frozen v0.5 6a3c0a3

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

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Open master c4d5139

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

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Frozen master 6638bd0

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

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

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

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

Added/updated 8 files


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help Creators and Submitter
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Wolfgang Maier

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Views: 13746   Downloads: 2133   Runs: 1

Created: 12th Mar 2021 at 13:41

Last updated: 2nd Oct 2024 at 11:01

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