Output data directory

EsViritu writes its primary tab-delimited outputs to the directory provided with -o/--output_dir. Each file is prefixed with your --sample name.

Location: <OUTPUT_DIR>/

Files

Detected Accessions

<SAMPLE>.detected_virus.info.tsv

  • Per-contig summary table of detected viral contigs.

  • Contains detection and quantification metrics for each contig.

Detected Genome Assemblies

<SAMPLE>.detected_virus.assembly_summary.tsv

  • Per-assembly summary table.

  • Aggregates contig-level results at the assembly level.

Taxonomic Profile

<SAMPLE>.tax_profile.tsv

  • Taxonomic profile table.

  • Assigns taxonomy to records based on average nucleotide identity to reference

  • See --species-threshold (default 0.90)

  • See --subspecies-threshold (default 0.95)

Coverage Windows

<SAMPLE>.virus_coverage_windows.tsv

  • Coverage in fixed windows across each reference contig.

  • Useful for visualizing coverage profiles and drops/gaps.

Notes

  • Temporary/intermediate files are written under <OUTPUT_DIR>/<SAMPLE>_temp/ (unless you set --temp). These include aligned .bam files,read-sharing comparisons, clustering summaries, coverm-like tables, and read ANI per contig. They will be removed automatically unless you run with --keep.

Column reference for main tables

SAMPLE.detected_virus.info.tsv

Column Type Description
sample_ID string Sample name provided via --sample.
Name string Virus name from database metadata.
description string Reference sequence description.
Length int Reference contig length (bp).
Segment string Segment identifier (if applicable).
Accession string Reference contig accession ID.
Assembly string Assembly name the contig belongs to.
Asm_length int Total assembly length (bp).
kingdom string Taxonomic rank.
phylum string Taxonomic rank.
tclass string Taxonomic class (named tclass to avoid keyword collision).
order string Taxonomic rank.
family string Taxonomic rank.
genus string Taxonomic rank.
species string Taxonomic rank.
subspecies string Taxonomic rank.
RPKMF float Reads per kilobase per million filtered reads: (read_count/(Length/1000)) / (filtered_reads_in_sample/1e6).
read_count int Number of reads aligned to the contig.
covered_bases int Number of bases with coverage > 0 on the contig.
mean_coverage float Mean read depth across the contig.
avg_read_identity float Average per-read alignment identity for the contig.
Pi float Average nucleotide diversity across covered positions.
filtered_reads_in_sample int Total filtered reads used for normalization.

SAMPLE.detected_virus.assembly_summary.tsv

Column Type Description
sample_ID string Sample name provided via --sample.
filtered_reads_in_sample int Total filtered reads used for normalization.
Assembly string Assembly name.
Asm_length int Total assembly length (bp).
kingdom string Taxonomic rank.
phylum string Taxonomic rank.
tclass string Taxonomic class (named tclass to avoid keyword collision).
order string Taxonomic rank.
family string Taxonomic rank.
genus string Taxonomic rank.
species string Taxonomic rank.
subspecies string Taxonomic rank.
read_count int Number of reads aligned across contigs in the assembly.
covered_bases int Number of bases with coverage > 0 across contigs in the assembly.
avg_read_identity float Mean read identity across contigs in the assembly.
Accession string Comma-separated list of accessions included.
Segment string Comma-separated list of segments included.
RPKMF float Assembly-level RPKMF using Asm_length.

SAMPLE.virus_coverage_windows.tsv

Column Type Description
Accession string Reference accession ID.
window_index int Window index (0–99).
window_start int 0-based start coordinate (inclusive).
window_end int 0-based end coordinate (exclusive).
average_coverage float Mean read depth across the window.

SAMPLE.tax_profile.tsv

Column Type Description
sample_ID string Sample name provided via --sample.
filtered_reads_in_sample int Total filtered reads used for normalization.
kingdom string Taxonomic rank.
phylum string Taxonomic rank.
tclass string Taxonomic class (named tclass to avoid keyword collision).
order string Taxonomic rank.
family string Taxonomic rank.
genus string Taxonomic rank.
species string Species classification; may be s__unclassified <genus> when avg_read_identity < --species-threshold.
subspecies string Subspecies classification; may be t__unclassified <species> when avg_read_identity < --subspecies-threshold.
read_count int Sum of reads aligned to assemblies contributing to this taxon.
RPKMF float Sum of RPKMF across assemblies in this taxon.
avg_read_identity float Mean read identity across assemblies in this taxon.
assembly_list string Comma-separated list of assemblies contributing to this row.