sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE

Workflow Type: Galaxy

COVID-19 sequence analysis on Illumina Amplicon PE data

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, CanCOGeN and some US state public health laboratories.

This workflow is also the subject of a Galaxy Training Network tutorial (currently a Work in Progress). It differs from this workflow in that it does not use lofreq and is aimed at rapid analysis of majority variants and lineage/clade assignment with pangolin and nextclade.

TODO:

  1. Add support for QC using negative and positive controls
  2. Integrate with phylogeny tools including IQTree and UShER (and possibly more).

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.
  • int?
Paired read collection for samples Paired read collection for samples FASTQ format Illumina Reads (Amplicon Protocol)
  • File[]
Primer BED Primer BED Primer BED file (from ARTIC project or similar)
  • File
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.
  • float?
Reference FASTA Reference FASTA SARS-CoV-2 reference genome (typically MN908947.3)
  • File

Steps

ID Name Description
5 fastp: Trimmed Illumina Reads toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+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/0.7.17.1
8 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3
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/1.3.1+galaxy2
12 Flatten Collection __FLATTEN__
13 ivar variants toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.3.1+galaxy2
14 ivar consensus toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.1+galaxy0
15 Quality Control Report toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+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/3.1.14+galaxy0
20 Nextclade toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/1.4.1+galaxy0

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_multifasta combined_multifasta n/a
  • File
all_samples_pangolin all_samples_pangolin n/a
  • File
all_samples_nextclade all_samples_nextclade n/a
  • File

Version History

v0.2.2 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.2.2


Open master 41edd94

v0.2.1 Created 5th Nov 2021 at 03:00 by WorkflowHub Bot

Updated to v0.2.1


Frozen master 1512b98

v0.2 Created 27th Oct 2021 at 15:45 by WorkflowHub Bot

Updated to v0.2


Frozen master 2ba0a73

v0.1 (earliest) Created 31st Aug 2021 at 03:01 by WorkflowHub Bot

Added/updated 7 files


Frozen master fe01ebf
help Creators and Submitter
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Additional credit

Peter van Heusden

Submitter
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Views: 2291   Downloads: 62

Created: 31st Aug 2021 at 03:01

Last updated: 21st Dec 2021 at 03:01

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