Enveomics collection

FastA.fragment.rb

Simulates incomplete (fragmented) drafts from complete genomes.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

FastA.fragment.rb --in in_file --out out_file --completeness float [opts]

§ Arguments

Input file*

 --in in_file  FastA file containing the complete sequences.

Output file*

 --out out_file  FastA to create.

Completeness*

 --completeness float  Fraction of genome completeness to simulate from 0 to 1.

Minimum length

 --minlen integer  Minimum fragment length to report.

Sorted

 --sorted   Keep fragments sorted as in the input file. By default, fragments are shuffled.

Quiet

 --quiet   Run quietly (no STDERR output).

* Mandatory.