freyja aggregate

Aggregates all demix data in RESULTS directory

freyja aggregate [OPTIONS] RESULTS

Options

--ext <ext>

file extension option, e.g. X.ext

--output <output>

name for aggregated results

Default:

aggregated_result.tsv

Arguments

RESULTS

Required argument

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Example Usage:

For rapid visualization of results, we also offer two utility methods for manipulating the “demixed” output files. The first is an aggregation method

freyja aggregate [directory-of-output-files] --output [aggregated-filename.tsv]

By default, the minimum genome coverage is set at 60 percent. To adjust this, the --mincov option can be used (e.g. --mincov 75.We also now allow the user to specify a file extension of their choosing, using the --ext option (for example, for demix outputs called X.output)

freyja aggregate [directory-of-output-files] --output [aggregated-filename.tsv] --ext output