Enveomics collection

ogs.core-pan.rb

Subsamples the genomes in a set of Orthology Groups (OGs) and estimates the trend of core genome and pangenome sizes.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.
• Ruby gem json.

§ Usage

ogs.core-pan.rb --ogs in_file [opts]

§ Arguments

Ogs*

 --ogs in_file  Input file containing the precomputed OGs.

Summary

 --summary out_file  Output file in tabular format with summary statistics.

Tab

 --tab out_file  Output file in tabular format.

Json

 --json out_file  Output file in JSON format.

Replicates

 --replicates integer  Number of replicates to estimate.

Threads

 --threads integer  Children threads to spawn.

Quiet

 --quiet   Run quietly (no STDERR output).

* Mandatory.