Output Files

The ViralFlow tool generates 2 types of output: specific and compiled.

Specific Outputs

For each sample in the analysis, a results directory will be created with the pattern prefix_results where the prefix is a code created from the fastq file name of the sample. Each directory has the following results:

File	Description
`prefix.all.fa.pango.out.csv`	Tabular file with the results of the pangolin tool
`prefix.ann.vcf`	File in TSV format (Tab separated value) with annotation of the variants made by the snpEff tool
`prefix.depth5.all.fa.nextclade.csv`	Tabular file with the results of the nextclade tool
`prefix.depth5.amb.fa`	Consensus genome with ambiguous nucleotides at multiple allele positions
`prefix.depth5.fa`	Consensus genome with majority nucleotides. Majority consensus, normally deposited in GISAID
`prefix.depth5.fa.algn`	Consensus genome aligned with reference genome (following same size, mafft –keeplenght)
`prefix.depth5.fa.algn.minor.fa`	Consensus genome with minority nucleotides
`prefix.depth5.fa.bc.intrahost.short.tsv`	Tabular file summarizing the genomic positions where intrahost variants are supported
`prefix.depth5.fa.bc.intrahost.tsv`	Tabular file with all information on intrahost variant positions
`prefix.mapped.R1.fq.gz`	FASTQ R1 file with mapped reads
`prefix.mapped.R2.fq.gz`	FASTQ R2 file with mapped reads
`prefix.metrics.genome.tsv`	Tabular file with mapping depth and coverage metrics
`prefix.fastp.html`	HTML file summarizing the results of the fastp tool
`prefix_snpEff_summary.html`	HTML file summarizing the results of the snpEff tool
`prefix.sorted.bam`	File with the sorted mapping of the sample reads against the reference genome
`prefix.tsv`	VCF-like file generated by iVar
`prefix.unmapped.R1.bam.fq`	FASTQ R1 file with unmapped reads
`prefix.unmapped.R2.bam.fq`	FASTQ R2 file with unmapped reads
`prefix.vcf`	VCF file
`metrics.alignment_summary_metrics`	Text file with a summary of various metrics from the mapping
`nextclade.errors.csv`	File reporting nextclade errors
`nextclade_gene_*.translation.fasta`	File with the proteins of each gene
`snpEff_genes.txt`	Tabular file with the number of variants and estimated impact per gene
`wgs`	Textual file with mapping metrics, including depth by region
`prefix_coveragePlot.png`	PNG file with graphical visualization of genome coverage
`prefix_coveragePlot.svg`	SVG file with graphical visualization of genome coverage
`prefix_coveragePlot.html`	HTML file with graphical visualization of genome coverage
`prefix_snpPlot.png`	PNG file with graphical visualization of SNPs
`prefix_snpPlot.svg`	SVG file with graphical visualization of SNPs
`prefix_snpPlot.html`	HTML file with graphical visualization of SNPs
`prefix_depthPlot.png`	PNG file with graphical visualization of depth
`prefix_depthPlot.svg`	SVG file with graphical visualization of depth
`prefix_depthPlot.html`	HTML file with graphical visualization of depth

Compiled Outputs

ViralFlow also generates compiled outputs that aggregate results across all samples:

File	Description
`assembly_statistics_summary.tsv`	Summary of assembly statistics for all samples
`alignment_metrics_summary.tsv`	Summary of alignment metrics for all samples
`all_consensus.fasta`	Concatenated consensus sequences for all samples
`intrahost_summary.tsv`	Compiled intrahost variant information for all samples