sars-cov-2-ont-artic-variant-calling/COVID-19-ARTIC-ONT
v0.3.1 (latest)

v0.3.1 (latest)

v0.3

v0.2.1

v0.2

v0.1 (earliest)

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Workflow Type: Galaxy

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much higher error rate than Illumina-sequenced reads and are therefor plagued more by false-positive variant calls, this workflow does make no attempt to handle amplicons affected by potential primer-binding site mutations.

SEEK ID: https://workflowhub.eu/workflows/111?version=5

Inputs

ID	Name	Description	Type
Maximum read length	Maximum read length	Discard reads that are longer than this length	int?
Minimum read length	Minimum read length	Discard reads that are shorter than this length	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
ONT-sequenced reads	ONT-sequenced reads	ONT reads from ARTIC assay with fastqsanger encoding	File[]
Primer binding sites info in BED format	Primer binding sites info in BED format	BED file containing (ARTIC) primer positions. For ARTIC primer schemes the file can be obtained from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources.	File

Steps

ID	Name	Description
5	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
6	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
7	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
8	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
9	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
10	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
11	Parse parameter value	param_value_from_file
12	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
13	BamLeftAlign	toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1
14	ivar trim	toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2
15	QualiMap BamQC	toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
16	medaka consensus tool	toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2
17	Filter failed	__FILTER_FAILED_DATASETS__
18	medaka variant tool	toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.3.2+galaxy1
19	medaka variant tool	toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.3.2+galaxy1
20	Flatten Collection	__FLATTEN__
21	bedtools Intersect intervals	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0
22	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
23	bcftools annotate	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
24	SnpEff eff covid19 version	toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
25	Lofreq filter	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
26	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3

Outputs

ID	Name	Description	Type
length_filtered_reads	length_filtered_reads	n/a	File
fastp_report	fastp_report	n/a	File
minimap2_mapped_reads	minimap2_mapped_reads	n/a	File
filtered_mapped_reads	filtered_mapped_reads	n/a	File
mapped_reads_stats	mapped_reads_stats	n/a	File
realigned_filtered_mapped_reads	realigned_filtered_mapped_reads	n/a	File
primer_trimmed_realigned_filtered_mapped_reads	primer_trimmed_realigned_filtered_mapped_reads	n/a	File
bamqc_raw_output	bamqc_raw_output	n/a	File
bamqc_html_output	bamqc_html_output	n/a	File
medaka_consensus_data	medaka_consensus_data	n/a	File
medaka_variants_general	medaka_variants_general	n/a	File
medaka_variants_pbs	medaka_variants_pbs	n/a	File
bamqc_raw_output_flattened	bamqc_raw_output_flattened	n/a	File
variants_pbs	variants_pbs	n/a	File
preprocessing_and_mapping_reports	preprocessing_and_mapping_reports	n/a	File
variants_combined	variants_combined	n/a	File
annotated_variants	annotated_variants	n/a	File
annotated_variants_stats	annotated_variants_stats	n/a	File
lofreq_filtered	lofreq_filtered	n/a	File
annotated_softfiltered_variants	annotated_softfiltered_variants	n/a	File