1.5.1

Viridian container

Main tool: Viridian

Code repository: Viridian

Additional tools:

• samtools: 1.21
• bcftools: 1.21
• htslib: 1.21
• ENA: 1.7.1
• ngmerge: 0.3
• vt: 0.577721
• racon: 1.5.0
• mummer: 4.0.1
• read-it-and-keep: 0.3.0
• cylon: commit hash 8b61712aaff9a674f497b6569312cd84bfc446b6 # March 6, 2025
• varifier: commit hash fc953baeb7d79d1ac78f341abc6536c74b96c904 # May 12, 2025
• minimap2: 2.29

Basic information on how to use this tool:

• executable: viridian
• help: --help
• version: --version
• description: Ultra-careful amplicon-aware viral assembly for tiled amplicon schemes.

Full documentation: Viridian wiki

Example Usage

To run on paired Illumina reads:

viridian run_one_sample \
  --tech illumina \
  --reads1 reads_1.fastq.gz \
  --reads2 reads_2.fastq.gz \
  --outdir OUT

Download reads with accession SRR12345678 and run:

viridian run_one_sample --run_accession SRR12345678 --outdir OUT

The sequencing tech and unpaired/paired is taken from the ENA metadata for each run.