# 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 |