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


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


ID Name Description
6 Read It and Keep
7 Rename reference to NC_045512.2
8 rename bed entries to NC_045512.2
9 Compose text parameter value
10 fastp: Trimmed Illumina Reads
11 BBTools: BBMap
12 Samtools stats
13 Samtools view
14 QualiMap BamQC
15 Final Processed BAM files
16 Flatten collection __FLATTEN__
17 ivar variants
18 ivar consensus
19 coverage
20 Quality Control Report
21 Annotated variants
22 Consensus genome (masked for depth)
23 combined_coverage
24 Concatenate datasets
25 threshold coverage


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
  • Peter van Heusden
  • Bradley W. Langhorst

Views: 1009

Created: 28th Jun 2023 at 12:42

Last updated: 30th Jun 2023 at 06:14

help Attributions


Total size: 53.8 KB
Powered by
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH