1) Setup inputs

All mess commands take as input one or multiple tables.

In this guide we are using mess test to execute all the workflow steps using a minimal example (shown below)

minimal_test.tsv

taxon   nb  cov_sim sample
staphylococcus_aureus   1   0.1 sample1
1290    1   0.1 sample2

The input file contains:

• Taxon/accession and nb columns for genome download
• Third column to calculate genome coverage for read simulation.
• sample column to map genomes to their respective sample

Other examples

Table

See coverage calculation for more details

Example

basesreadstax_abundanceseq_abundancecoverage

taxon	nb	bases
1280	1	28213610
pseudomonas_aeruginosa	1	62644040

taxon	nb	reads
1280	1	94045
pseudomonas_aeruginosa	1	208813

taxon	nb	tax_abundance
1280	1	0.5
pseudomonas_aeruginosa	1	0.5

taxon	nb	seq_abundance
1280	1	0.32
pseudomonas_aeruginosa	1	0.68

taxon	nb	cov_sim
1280	1	10
pseudomonas_aeruginosa	1	10

Directory

If you want to simulate multiple samples at once, you can point to a directory with multiple tables (one for each sample, with the sample name in the file name).

Example

📂sequencing_run
┣ 📜sample1.tsv
┣ 📜sample2.tsv
┗ 📜sample3.tsv

Or you can aggregate all sample info in one table

Example

taxon	nb	cov_sim	sample
staphylococcus_aureus	1	10	sample1
1290	1	10	sample2
562	1	10	sample3