Workflow Type: Galaxy
Open
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.
Inputs
ID | Name | Description | Type |
---|---|---|---|
ARTIC primer BED | ARTIC primer BED | n/a |
|
Maximum read length | Maximum read length | Discard reads that are longer than this length |
|
Minimum read length | Minimum read length | Discard reads that are shorter than this length |
|
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 |
|
ONT-sequenced reads | ONT-sequenced reads | ONT reads from ARTIC assay with fastqsanger encoding |
|
Steps
ID | Name | Description |
---|---|---|
5 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
6 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 |
7 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 |
8 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1 |
9 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
10 | BamLeftAlign | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1 |
11 | medaka consensus tool | toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2 |
12 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
13 | medaka variant tool | toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy3 |
14 | Flatten Collection | __FLATTEN__ |
15 | Lofreq filter | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 |
16 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 |
17 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
18 | SnpEff eff covid19 version | toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
length_filtered_reads | length_filtered_reads | n/a |
|
fastp_report | fastp_report | n/a |
|
minimap2_mapped_reads | minimap2_mapped_reads | n/a |
|
filtered_mapped_reads | filtered_mapped_reads | n/a |
|
primer_trimmed_filtered_mapped_reads | primer_trimmed_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 |
|
medaka_consensus_data | medaka_consensus_data | n/a |
|
bamqc_raw_output | bamqc_raw_output | n/a |
|
bamqc_html_output | bamqc_html_output | n/a |
|
medaka_variant_calls | medaka_variant_calls | n/a |
|
bamqc_raw_output_flattened | bamqc_raw_output_flattened | n/a |
|
soft_filtered_variants | soft_filtered_variants | n/a |
|
preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
|
soft_filtered_variants_fixed | soft_filtered_variants_fixed | n/a |
|
annotated_variants | annotated_variants | n/a |
|
annotated_variants_stats | annotated_variants_stats | n/a |
|
Version History
Version 1 (earliest) Created 1st Mar 2021 at 12:11 by WorkflowHub Sandbox Bot
Added/updated 8 files
Open
master
26abc4a
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
License
Activity
Views: 1367 Downloads: 219
Created: 1st Mar 2021 at 12:11
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
None