SARS-CoV-2 Illumina Amplicon pipeline - SANBI - v1.2
Version 1

Workflow Type: Galaxy

SARS-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
  • int?
Minimum quality score to call base Minimum quality score to call base n/a
  • int?
Paired read collection for samples Paired read collection for samples n/a
  • File[]
Primer BED Primer BED n/a
  • File
Read fraction to call variant Read fraction to call variant n/a
  • float?
Reference FASTA Reference FASTA n/a
  • File

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
  • File
ivar_variants_tabular ivar_variants_tabular n/a
  • File
bamqc_report_html bamqc_report_html n/a
  • File
snpeff_annotated_vcf snpeff_annotated_vcf n/a
  • File
ivar_consensus_genome ivar_consensus_genome n/a
  • File
combined_coverage combined_coverage n/a
  • File
combined_multifasta combined_multifasta n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File

Version History

Version 1 (earliest) Created 28th Jun 2023 at 12:42 by Peter van Heusden

Initial commit


Open master 8c1331c
help Creators and Submitter
Creators
  • Peter van Heusden
  • Bradley W. Langhorst
Submitter
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Views: 1009

Created: 28th Jun 2023 at 12:42

Last updated: 30th Jun 2023 at 06:14

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