Quick start commands

Navigate to Tool 2 /genomics/home/vol-genomics/genome_tools/Tool_2

  1. Deposit the assembled genomes of the strains you want to compare in the input_genomes folder.
  2. Deposit the sequences for mass screening in the input_custom_seqs folder.
  3. Set up a stable connection using the command tmux new -s 'name'
  4. Initiate Tool 2 using the command nextflow run tool_2.nf [options]

Your results will be saved in /Tool_2/output_tool2

Options

Term Description Default
--customSeq 'xxx' name chosen by user test
--identity 'yy' minimum DNA %identity 75
--coverage 'zz' minimum DNA %coverage 0

Example

nextflow run tool_2.nf --customSeq '12P' --identity '90' --coverage '75'

Tool 2 will run using 75% minimum DNA coverage and 90% minimum DNA identity, and name the output folder 12P.

Tip

To view the Quick start instructions from the command line use:

nextflow run tool_2.nf --help