Running EsViritu

You might run this as part of a bash script, snakemake pipeline, do your own upstream read processing, etc, but these are the basic instructions.

Required inputs:

-r reads file FASTQ format (can be gzipped .gz)

-s sample name

-o output directory (may be shared with other samples)

Activate the conda environment:

conda activate EsViritu

Individual samples can be run with the python script. E.g.:

Basic run with 1 .fastq file:

EsViritu -r /path/to/reads/myreads.fastq -s sample_ABC -o myproject_EsViritu1 -p unpaired

Using paired end input .fastq files. Must be exactly 2 files.

EsViritu -r /path/to/reads/myreads.R1.fastq /path/to/reads/myreads.R2.fastq -s sample_ABC -o myproject_EsViritu1 -p paired

With pre-filtering steps:

EsViritu -r /path/to/reads/myreads.fastq -s sample_ABC -o myproject_EsViritu1 -q True -f True -p unpaired

Help menu

EsViritu -h

Making a summary report for a batch of samples

Run the batch summary script to collate reports from several sequencing libraries in a project:

Example:

Activate conda environment: conda activate EsViritu

Then run the summarize_esv_runs command with the relative path to the output directory as the only argument:

summarize_esv_runs myproject_EsViritu1

This command will generate the tables myproject_EsViritu1.detected_virus.info.tsv, myproject_EsViritu1.detected_virus.assembly_summary.tsv, myproject_EsViritu1.tax_profile.tsv and the reactable myproject_EsViritu1.batch_detected_viruses.html, which summarize information about all the samples in the given directory.