sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE
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Workflow Type: Galaxy
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Tests Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Minimum quality score to call base | Minimum quality score to call base | Minimum base quality score to count a base towards the sequence consensus. |
|
| Paired read collection for samples | Paired read collection for samples | FASTQ format Illumina Reads (Amplicon Protocol) |
|
| Primer BED | Primer BED | Primer BED file (from ARTIC project or similar) |
|
| Read fraction to call variant | Read fraction to call variant | Specify the proportion of reads that need to agree with each other to call a variant. This is a floating point value between 0 and 1. |
|
| Reference FASTA | Reference FASTA | SARS-CoV-2 reference genome (typically MN908947.3) |
|
| Version of pangolin-data to use | Version of pangolin-data to use | You can select any pangolin-data version set up on this Galaxy server that should be used at the pangolin lineage assignment step. If you don't see any options to select from, this means the server doesn't offer any pangolin-data versions. In this case or if you don't want to bother with version selection, leave this input blank and the workflow will use pangolin-data version 1.37 bundled with pangolin. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0 |
| 7 | Rename reference to NC_045512.2 | If the reference is named MN908947.3 (Genbank name of SARS-CoV-2 reference genome), rename it to NC_045512.2 (RefSeq name of SARS-CoV-2 reference genome) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3 |
| 8 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 9 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 |
| 10 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 11 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8 |
| 12 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1 |
| 13 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0 |
| 14 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy1 |
| 15 | Flatten collection | __FLATTEN__ |
| 16 | ivar variants | toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.4+galaxy0 |
| 17 | ivar consensus | toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0 |
| 18 | Quality Control Report | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
| 19 | Annotated variants | toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 |
| 20 | Consensus genome (masked for depth) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3 |
| 21 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 |
| 22 | Nextclade | toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0 |
| 23 | Pangolin | toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3.4+galaxy3 |
| 24 | Pangolin | toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3.4+galaxy3 |
| 25 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| primer_trimmed_bam | primer_trimmed_bam | n/a |
|
| ivar_variants_tabular | ivar_variants_tabular | n/a |
|
| bamqc_report_html | bamqc_report_html | n/a |
|
| snpeff_annotated_vcf | snpeff_annotated_vcf | n/a |
|
| ivar_consensus_genome | ivar_consensus_genome | n/a |
|
| combined_multifasta | combined_multifasta | n/a |
|
| all_samples_nextclade | all_samples_nextclade | n/a |
|
| all_samples_pangolin | all_samples_pangolin | n/a |
|
Version History
v0.4v0.1 (earliest) Created 31st Aug 2021 at 03:01 by WorkflowHub Bot
Added/updated 7 files
Frozen
masterfe01ebf
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Views: 14373 Downloads: 36883 Runs: 3
Created: 31st Aug 2021 at 03:01
Last updated: 19th Aug 2025 at 09:57
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