sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA
v0.5.3 (latest)

v0.5.3 (latest)

v0.5.2

v0.5.1

v0.5

v0.4.2

v0.4.1

v0.4

v0.3

v0.2

v0.1 (earliest)

Workflow Type: Galaxy

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 tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.

SEEK ID: https://workflowhub.eu/workflows/110?version=10

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	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	#main/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	#main/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	#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
Read removal maximum AF	#main/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	#main/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	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1
9	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
10	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
11	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
12	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
13	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
14	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5
15	Insert indel qualities	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
16	ivar trim	toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0
17	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2
18	QualiMap BamQC	toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
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	ivar removereads	toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.2+galaxy0
23	Flatten collection	__FLATTEN__
24	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2
25	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
26	bcftools annotate	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3
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/1.15.1+galaxy3
30	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
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
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_json_report	#main/fastp_json_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_filter_passing_variants	#main/lost_filter_passing_variants	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_1_filtered	#main/preliminary_variants_1_filtered	n/a	File
preliminary_variants_2	#main/preliminary_variants_2	n/a	File
preliminary_variants_2_filtered	#main/preliminary_variants_2_filtered	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_fixed	#main/variants_fixed	n/a	File
variants_fixed_header	#main/variants_fixed_header	n/a	File
variants_fixed_partial	#main/variants_fixed_partial	n/a	File