Outputs

  1. Overview
  2. Alignment Files
  3. Assembly Files
  4. Metagenome Files
    1. Sourmash Outputs
    2. Visualizations
  5. Quality Files
    1. Read QC
    2. Read Alignment
    3. Assembly Selection
  6. Mapped Reads
  7. Reference selection
  8. Summary Files
    1. VAPER Summary Columns

Overview

Below is an overview of the standard outputs produced by VAPER.

`${outdir}` 
├── `${sample}`
│   ├── align
│   │   ├── `${reference}`.fa
│   │   ├── `${reference}`.fa.fai
│   │   ├── `${sample}-${reference}`.bam
│   │   └── `${sample}-${reference}`.bam.bai
│   ├── assembly
│   │   └── `${sample}-${reference}`.fa.gz
│   ├── metagenome
│   │   ├── `${sample}`.all-taxa.csv.gz
│   │   ├── `${sample}`.html
│   │   ├── `${sample}`.sm-meta.csv
│   │   └── `${sample}`.taxa-plot.jpg
│   ├── qc
│   │   ├── `${sample}-${reference}`.coverage.txt
│   │   ├── `${sample}-${reference}`.read-list.txt
│   │   ├── `${sample}-${reference}`.stats.txt
│   │   ├── `${sample}`.condense_dist.csv
│   │   ├── `${sample}`.condense_summary.csv
│   │   ├── `${sample}`.fastp.json
│   │   ├── `${sample}`_1_fastqc.html
│   │   ├── `${sample}`_1_fastqc.zip
│   │   ├── `${sample}`_2_fastqc.html
│   │   └── `${sample}`_2_fastqc.zip
│   ├── reads
│   │   ├── `${sample}-${reference}`_R1.fastq.gz
│   │   └── `${sample}-${reference}`_R2.fastq.gz
│   ├── ref-select
│   │   ├── `${sample}`.acc-ref.paf
│   │   ├── `${sample}`.denovo.fa
│   │   └── `${sample}`.ref-summary.csv
│   └── summary
│       └── `${sample}-${reference}`.summaryline.csv
├── VAPER-summary.csv
├── multiqc
└── pipeline_info

Alignment Files

Read alignments and the corresponding reference and index files are provided for visualization tools like IGV.

├── align
│   ├── `${reference}`.fa
│   ├── `${reference}`.fa.fai
│   ├── `${sample}-${reference}`.bam
│   └── `${sample}-${reference}`.bam.bai

Assembly Files

Final assemblies based on selected references.

├── assembly
│   └── `${sample}-${reference}`.fa.gz

Metagenome Files

Multiple metagenomic outputs are provided. See descriptions below:

├── metagenome
│   ├── `${sample}`.all-taxa.csv.gz
│   ├── `${sample}`.html
│   ├── `${sample}`.sm-meta.csv
│   └── `${sample}`.taxa-plot.jpg

Sourmash Outputs

  • ${sample}.all-taxa.csv.gz is the summary file generated by sourmash gather
  • ${sample}.sm-meta.csv is the summary file generated by sourmash taxa metagenome`

Visualizations

  • ${sample}.html is a Krona plot generated from ${sample}.sm-meta.csv
  • ${sample}.taxa-plot.jpg shows the relative abundance of all classified sequences (excludes unclassified). Classifications with < 1% relative abundance are grouped under “Other”.

Quality Files

Files related to quality control are saved to a common directory. See descriptions below:

├── qc
│   ├── `${sample}-${reference}`.coverage.txt
│   ├── `${sample}-${reference}`.read-list.txt
│   ├── `${sample}-${reference}`.stats.txt
│   ├── `${sample}`.condense_dist.csv
│   ├── `${sample}`.condense_summary.csv
│   ├── `${sample}`.fastp.json
│   ├── `${sample}`_1_fastqc.html
│   ├── `${sample}`_1_fastqc.zip
│   ├── `${sample}`_2_fastqc.html
│   └── `${sample}`_2_fastqc.zip

Read QC

  • ${sample}.fastp.json is the QC summary of the raw and quality filtered reads provided by fastp.
  • ${sample}_{1,2}_fastqc.* are the QC files for the fastp-controlled reads generated by FASTQC.

Read Alignment

${sample}-${reference}.coverage.txt and ${sample}-${reference}.stats.txt describe read mapping quality metrics for each reference genome.

Assembly Selection

${sample}.condense_dist.csv and ${sample}.condense_summary.csv are the outputs generated by vaper-condense.py and used to determine whether two assemblies should be merged.

Mapped Reads

Reads that map to each reference genome are exported for downstream use.

├── reads
│   ├── `${sample}-${reference}`_R1.fastq.gz
│   └── `${sample}-${reference}`_R2.fastq.gz

Reference selection

Files related to reference selection are saved to a common directory. See descriptions below:

│   ├── ref-select
│   │   ├── `${sample}`.acc-ref.paf
│   │   ├── `${sample}`.denovo.fa
│   │   └── `${sample}`.ref-summary.csv
  • ${sample}.denovo.fa is the de novo assembly generated by shovill when using accurate reference selection mode.
  • ${sample}.acc-ref.paf is the alignment file generated by minimap2 between the de novo assembly and the references, when using accurate reference selection mode.
  • ${sample}.ref-summary.csv is a summary of the genome fraction of each reference covered by the de novo assembly contigs.

Summary Files

Summary files are provided both individually (by sample) or collectively (by run)

│   └── summary
│       └── `${sample}-${reference}`.summaryline.csv
├── VAPER-summary.csv
  • ${sample}-${reference}.summaryline.csv is the individual summary for each sample-reference combo and may lack columns present in the combined summary.
  • VAPER-summary.csv is the combined summary for all samples included on a run.

VAPER Summary Columns

[!NOTE] The descriptions below only include the default VAPER columns. Additional columns may appear when using the EPITOME reference set, including SPECIES, COLLECTIONDATE, GEOGRAPHICREGION, etc. These columns include information about the sequences that were used to create the reference genome (as listed in NCBI or GISAID). See the EPITOME wiki for more info.

Column Name Description
ID The sample ID provided in the samplesheet followed by the sample replicate number (e.g., _T1).
REFERENCE Name of the reference genome used to create the sample assembly.
SEGMENT The genome segment name or number. Non-segmented viruses will be reported as wg (whole genome) when using the default reference set.
ASSEMBLY_VARIANT Numbered version of an assembly. This should always be 1 of 1 unless there are multiple assemblies associated with a single species-segment combination for a sample. Multiple assemblies may arise from same-species co-infections or fragmented de novo assemblies affecting reference selection.
ASSEMBLY_QC Automated reporting of assembly quality (PASS or FAIL) based on reference genome fraction (--qc_genfrac) and reference depth of coverage (--qc_depth).
ASSEMBLY_QC_REASON Explanation for QC failure.
ASSEMBLY_LENGTH Number of nucleotides in the sample assembly (includes non-ATCG).
REF_LENGTH Number of nucleotides in the reference assembly (includes non-ATCG).
ASSEMBLY_EST_DEPTH Estimated number of reads supporting each position in the sample assembly.
ASSEMBLY_GEN_FRAC The proportion of nucleotide positions in the reference genome present in the sample assembly (excludes missing nucleotides).
ASSEMBLY_SUBS Number of nucleotide substitutions in the sample compared to the reference.
ASSEMBLY_DEL Number of nucleotide deletions in the sample assembly compared to the reference.
ASSEMBLY_INS Number of nucleotide insertions in the sample assembly compared to the reference.
ASSEMBLY_MISSING Number of unassigned nucleotides (N) in the sample assembly compared to the reference.
ASSEMBLY_NON_ACGTN Number of nucleotides assigned as something other than A, C, G, T, or N in the sample assembly compared to the reference.
ASSEMBLY_TERMINI_GAPS Number of terminal nucleotides in the reference that are missing in the sample assembly. Nextclade reports these separately from missing nucleotides.
PERC_READS_MAPPED Percent of clean reads that mapped to the reference genome.
PERC_BASES_MAPPED Percent of bases in the clean reads that mapped to the reference genome.
MEAN_MAPPED_READ_LENGTH Average length of the clean reads that mapped to the reference genome.
MEAN_MAPPED_READ_QUALITY Average Phred score of the clean reads that mapped to the reference genome.
TOTAL_READS_CLEAN Number of clean reads (R1 + R2).
TOTAL_BASES_CLEAN Number of bases in the clean reads (R1 + R2).
READ1_MEAN_LENGTH_CLEAN Average length of the clean forward reads.
READ2_MEAN_LENGTH_CLEAN Average length of the clean reverse reads.
Q30_RATE_CLEAN Percentage of bases in the clean reads that have a Phred score of 30 or greater.
TOTAL_READS_RAW Number of raw reads (R1 + R2).
TOTAL_BASES_RAW Number of bases in the raw reads (R1 + R2).
READ1_MEAN_LENGTH_RAW Average length of the raw forward reads.
READ2_MEAN_LENGTH_RAW Average length of the raw reverse reads.
Q30_RATE_RAW Percentage of bases in the raw reads that have a Phred score of 30 or greater.
SPECIES_SUMMARY Relative abundance of viral species detected in the sample reads using Sourmash. Species with ≤ 1% relative abundance are categorized as Other. Relative abundance is calculated using only the classified sequences.