sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA
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Workflow Type: Galaxy

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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.

SEEK ID: https://workflowhub.eu/workflows/110?version=9

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