SARS-CoV-2 Illumina Amplicon pipeline - SANBI - v1.2 Version 1
Download RO Crate
Run on usegalaxy.euSARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Max Viz. Coverage Threshold | Max Viz. Coverage Threshold | n/a |
|
| Minimum quality score to call base | Minimum quality score to call base | n/a |
|
| Paired read collection for samples | Paired read collection for samples | n/a |
|
| Primer BED | Primer BED | n/a |
|
| Read fraction to call variant | Read fraction to call variant | n/a |
|
| Reference FASTA | Reference FASTA | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Read It and Keep | toolshed.g2.bx.psu.edu/repos/iuc/read_it_and_keep/read_it_and_keep/0.2.2+galaxy0 |
| 7 | Rename reference to NC_045512.2 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
| 8 | rename bed entries to NC_045512.2 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
| 9 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 10 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
| 11 | BBTools: BBMap | toolshed.g2.bx.psu.edu/repos/iuc/bbtools_bbmap/bbtools_bbmap/1.0.0+galaxy4 |
| 12 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 13 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 |
| 14 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
| 15 | Final Processed BAM files | toolshed.g2.bx.psu.edu/repos/iuc/samtools_ampliconclip/samtools_ampliconclip/1.13 |
| 16 | Flatten collection | __FLATTEN__ |
| 17 | ivar variants | toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.3.1+galaxy2 |
| 18 | ivar consensus | toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.1+galaxy0 |
| 19 | coverage | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0 |
| 20 | Quality Control Report | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
| 21 | Annotated variants | toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 |
| 22 | Consensus genome (masked for depth) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
| 23 | combined_coverage | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 24 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 25 | threshold coverage | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
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_coverage | combined_coverage | n/a |
|
| combined_multifasta | combined_multifasta | n/a |
|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
Version History
Version 1 (earliest) Created 28th Jun 2023 at 12:42 by Peter van Heusden
Initial commit
Open
master8c1331c
Creators and Submitter
Views: 1501
Created: 28th Jun 2023 at 12:42
Last updated: 30th Jun 2023 at 06:14
Tags AttributionsNone
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https://orcid.org/0000-0001-6553-5274
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Public web page: https://www.sanbi.ac.za/
