Simple COVID-19 - PE Variation
7.0 (earliest)

1.0 (latest)

7.0 (earliest)

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Workflow Type: Galaxy

Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured

Associated Tutorial

This workflows is part of the tutorial Simple COVID-19 - PE Variation, available in the GTN

Tutorial Author(s): Marius van den Beek, Dave Clements, Daniel Blankenberg, Anton Nekrutenko

Tutorial Contributor(s): Wolfgang Maier

SEEK ID: https://dev.workflowhub.eu/workflows/1074?version=1

ID	Name	Description	Type
NC_045512.2 fasta file	#main/NC_045512.2 fasta file	Contains SARS-CoV-2 reference sequence	File
SRA Manifest	#main/SRA Manifest	n/a	File

ID	Name	Description
2	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1
3	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
4	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
5	MarkDuplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
6	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
7	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
8	Insert indel qualities	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
9	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
10	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
11	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
12	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0

ID	Name	Description	Type
MultiQC Report PE	#main/MultiQC Report PE	n/a	File
Realigned Alignments with Indel Qualities	#main/Realigned Alignments with Indel Qualities	n/a	File
SnpSift tabular output	#main/SnpSift tabular output	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File