sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA
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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://workflowhub.eu/workflows/110?version=2

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	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	#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

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
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_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_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	#main/variants	n/a	File
variants_fixed_header	#main/variants_fixed_header	n/a	File