sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA
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Tests 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.
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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 |
|
| 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 |
|
| 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. |
|
| 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. |
|
| 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 |
|
| Paired Collection | Paired Collection | Illumina reads from ARTIC assay with fastqsanger encoding |
|
| 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. |
|
| 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. |
|
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 |
|
| fastp_json_report | fastp_json_report | n/a |
|
| fastp_reads_output | fastp_reads_output | n/a |
|
| mapped_reads | mapped_reads | n/a |
|
| filtered_mapped_reads | filtered_mapped_reads | n/a |
|
| mapped_reads_stats | mapped_reads_stats | n/a |
|
| realigned_primer_trimmed_filtered_mapped_reads | realigned_primer_trimmed_filtered_mapped_reads | n/a |
|
| realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals | realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals | n/a |
|
| primer_trimmed_filtered_mapped_reads | primer_trimmed_filtered_mapped_reads | n/a |
|
| preliminary_variants_1 | preliminary_variants_1 | n/a |
|
| bamqc_raw_output | bamqc_raw_output | n/a |
|
| bamqc_html_output | bamqc_html_output | n/a |
|
| filtered_preliminary_variants | filtered_preliminary_variants | n/a |
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| preliminary_variants_1_filtered | preliminary_variants_1_filtered | n/a |
|
| bamqc_raw_output_flattened | bamqc_raw_output_flattened | n/a |
|
| amplicon_removal_output | amplicon_removal_output | n/a |
|
| preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
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| preprocessing_and_mapping_plots | preprocessing_and_mapping_plots | n/a |
|
| preliminary_variants_2 | preliminary_variants_2 | n/a |
|
| variants_fixed_partial | variants_fixed_partial | n/a |
|
| preliminary_variants_2_filtered | preliminary_variants_2_filtered | n/a |
|
| lost_filter_passing_variants | lost_filter_passing_variants | n/a |
|
| variants_fixed | variants_fixed | n/a |
|
| variants_fixed_header | variants_fixed_header | n/a |
|
| annotated_variants | annotated_variants | n/a |
|
| annotated_variants_stats | annotated_variants_stats | n/a |
|
| annotated_softfiltered_variants | annotated_softfiltered_variants | n/a |
|
Version History
v0.5.3 (latest) Created 7th Oct 2024 at 16:31 by WorkflowHub Bot
Updated to v0.5.3
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v0.5.326a4baa
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
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master865c5cb
Creators and Submitter
Citation
Maier, W. (2022). sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.110.7
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Views: 13754 Downloads: 2134 Runs: 1
Created: 12th Mar 2021 at 13:41
Last updated: 2nd Oct 2024 at 11:01
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https://orcid.org/0000-0002-9464-6640
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
Teams: usegalaxy-eu, GalaxyProject SARS-CoV-2
Organizations: European Galaxy Team
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Workflows developed by or used by BY-COVID project.
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...
