iLund4u
Home page and documentation: https://art-egorov.github.io/ilund4u/
The Atkinson Lab 4U | AE
-------- PROTEOME MODE --------
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    COMMAND-LINE PARAMETERS
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[MANDATORY ARGUMENTS]
-gff <path>
    Path to a query proteome gff file.
    (designed to handle pharokka/prokka produced annotation files).
-db <path>
    Path to iLund4u database.
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[OPTIONAL ARGUMENTS | DATA PROCESSING]
-ncg, --non-circular-genomes
    Consider tje query genome as non-circular. This means that first
    and last proteins won't be considered to be neighbours.
    [default: circular]
Note: MMseqs arguments below are used for assigning homology
      group for each protein in your query proteome.
-msqc, --mmseqs-query-cov <float>
    MMseqs search query coverage cutoff [default: 0.65]
-mstc, --mmseqs-target-cov <float>
    MMseqs search query coverage cutoff [default: 0.65]
-msf, --mmseqs-fident <float>
    MMseqs search fident (fraction of identical matches) cutoff
    [default: 0.2]
-mse, --mmseqs-evalue
    MMseqs search evalue cutoff [default: 1e-5]
-fm, --fast-mmseqs
    MMseqs search only against a database of representative sequences.
    [default: False]
-rnf, --report-not-flanked
    Report in results hotspots that have flanked conserved genes only on one
    side (located on the end of non-circular sequences) [default: False]
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[OPTIONAL ARGUMENTS | OTHERS]
-o <name>
    Output dir name. It will be created if it does not exist.
	[default: ilund4u_{current_date}; e.g. ilund4u_2022_07_25-20_41]
-c <standard|<file.cfg>
    Path to a configuration file or name of a premade config file
    [default: standard]
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[MISCELLANEOUS ARGUMENTS]
--debug
    Provide a detailed stack trace for debugging purposes.
-q, --quiet
    Don't show progress messages.
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