sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE
Version 1

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
Paired read collection for samples Paired read collection for samples FASTQ format Illumina Reads (Amplicon Protocol) n/a
Reference FASTA Reference FASTA SARS-CoV-2 reference genome (typically MN908947.3) n/a
Primer BED Primer BED Primer BED file (from ARTIC project or similar) n/a
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. n/a
Minimum quality score to call base Minimum quality score to call base Minimum base quality score to count a base towards the sequence consensus. n/a
input_bam input_bam runtime parameter for tool ivar trim n/a
primer primer runtime parameter for tool ivar trim n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a
input1 input1 runtime parameter for tool Pangolin n/a
input_fasta input_fasta runtime parameter for tool Nextclade n/a

Steps

ID Name Description
0 Paired read collection for samples FASTQ format Illumina Reads (Amplicon Protocol)
1 Reference FASTA SARS-CoV-2 reference genome (typically MN908947.3)
2 Primer BED Primer BED file (from ARTIC project or similar)
3 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.
4 Minimum quality score to call base Minimum base quality score to count a base towards the sequence consensus.
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/3.1.11+galaxy0
20 Nextclade toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/1.2.3+galaxy0

Outputs

ID Name Description Type
output_paired_coll output_paired_coll n/a input
report_html report_html n/a html
report_json report_json n/a json
output output n/a input
bam_output bam_output n/a bam
output output n/a tabular
outputsam outputsam n/a input
raw_data raw_data n/a input
output_html output_html n/a html
output_bam output_bam n/a bam
output output n/a input
output_variants_tabular output_variants_tabular n/a tabular
output_variants_vcf output_variants_vcf n/a vcf
consensus consensus n/a fasta
stats stats n/a input
html_report html_report n/a html
snpeff_output snpeff_output n/a vcf
statsFile statsFile n/a html
output output n/a input
out_file1 out_file1 n/a input
output1 output1 n/a tabular
report_tsv report_tsv n/a tabular
help Creators and Submitter
Creator
  • Peter van Heusden
Submitter
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Views: 86   Downloads: 9

Created: 31st Aug 2021 at 03:01

Last used: 25th Sep 2021 at 17:44

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Version 1 Created 31st Aug 2021 at 03:01 by WorkflowHub Bot

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