Workflow Type: Galaxy
Frozen
Frozen
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.
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 | 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 |
|
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 |
|
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 |
---|---|---|---|
fastp_html_report | fastp_html_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 |
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primer_trimmed_filtered_mapped_reads | primer_trimmed_filtered_mapped_reads | n/a |
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mapped_reads_stats | mapped_reads_stats | n/a |
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realigned_primer_trimmed_filtered_mapped_reads | realigned_primer_trimmed_filtered_mapped_reads | n/a |
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realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals | realigned_primer_trimmed_filtered_mapped_reads_with_indel_quals | n/a |
|
bamqc_html_output | bamqc_html_output | n/a |
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bamqc_raw_output | bamqc_raw_output | n/a |
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preliminary_variants_1 | preliminary_variants_1 | n/a |
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bamqc_raw_output_flattened | bamqc_raw_output_flattened | n/a |
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filtered_preliminary_variants | filtered_preliminary_variants | n/a |
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preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
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preprocessing_and_mapping_plots | preprocessing_and_mapping_plots | n/a |
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amplicon_removal_output | amplicon_removal_output | n/a |
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preliminary_variants_2 | preliminary_variants_2 | n/a |
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lost_variants_tmp | lost_variants_tmp | n/a |
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lost_variants | lost_variants | n/a |
|
variants | variants | 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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v0.5.3
26a4baa
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
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master
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Creators and Submitter
Creator
Additional credit
Wolfgang Maier
Submitter
License
Activity
Views: 13746 Downloads: 2133 Runs: 1
Created: 12th Mar 2021 at 13:41
Last updated: 2nd Oct 2024 at 11:01
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