Options

For an explanation of individual options, see FALCON Manual. Also see Options-Available.

Setting options

In .cfg file

At the command-line, the config files have standard .ini or .cfg format. E.g.

[General]
foo_option=--bar1 --bar2

Many options can take a list (space-separated) of sub-options for a specific sub-tool, e.g.

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4
fc_ovlp_to_graph_option = --min_len 10 -- min_idt 0.70
overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20
pa_dbsplit_option=-x500 -s1000 -a

Via smrtlink GUI.

(This section will not make sense until you see the GUI.)

Within "Advanced Analysis Parameters", in the Assembly FALCON cfg overrides box, you can set any options in a semicolon-separated list, case-insensitive, e.g.

pa_dbsplit_option=-x500 -s1000 -a; falcon_sense_option=--output_multi --min_idt 0.70 --min_cov 4;

Options for specific tools

You can get this via --help on the command-line. Or just look at the options and defaults for any tool.