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README.md

Viridian container

Main tool: Viridian

Code repository: Viridian

Additional tools:

  • samtools: 1.20
  • bcftools: 1.20
  • htslib: 1.20
  • ENA: 1.7.1
  • ngmerge: 0.3
  • vt: 0.577721
  • racon: 1.5.0
  • mummer: 4.0.0
  • read-it-and-keep: 0.3.0
  • cylon: commit hash 57d559a76254b0b95785f7c02fa58ef806713e01
  • varifier: commit hash 8bc8726ed3cdb337dc47b62515e709759e451137
  • minimap2: 2.28

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.