sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE
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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) |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
| 6 | 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/1.1.1 |
| 7 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
| 8 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4 |
| 9 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 10 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
| 11 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0 |
| 12 | Flatten collection | __FLATTEN__ |
| 13 | ivar variants | toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.2+galaxy1 |
| 14 | ivar consensus | toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0 |
| 15 | Quality Control Report | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 16 | Annotated variants | toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 |
| 17 | Consensus genome (masked for depth) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
| 18 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 19 | Pangolin | toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy1 |
| 20 | Nextclade | toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0 |
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_pangolin | all_samples_pangolin | n/a |
|
| all_samples_nextclade | all_samples_nextclade | n/a |
|
Version History
v0.3.1 (latest) Created 31st Jul 2025 at 03:02 by WorkflowHub Bot
Updated to v0.3.1
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v0.3.16b3dbdd
v0.1 (earliest) Created 31st Aug 2021 at 03:01 by WorkflowHub Bot
Added/updated 7 files
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masterfe01ebf
Creators and Submitter
License
Activity
Views: 12269 Downloads: 7984 Runs: 3
Created: 31st Aug 2021 at 03:01
Last updated: 19th Aug 2025 at 09:57
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https://orcid.org/0000-0001-6553-5274
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