COVID-19-PE-ARTIC-ILLUMINA (v0.1)
Version 1

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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.

SEEK ID: https://dev.workflowhub.eu/workflows/143?version=1

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 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
22 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19

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
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
Creators
Not specified
Additional credit

Wolfgang Maier

Submitter
License
MIT License
Activity

Views: 1655   Downloads: 342

Created: 1st Mar 2021 at 12:11

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Total size: 108 KB
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