The compact command¶

The organelle assembler’s compact rebuild the gml file containing the compacted version of the assembling graph from a previously asssembled dataset.

command prototype¶

usage: oa buildgraph [-h]
                     [--back ORGASM:BACK]
                     index [output]

positional arguments¶

index¶: index root filename (produced by the oa index command)

output¶: output prefix

optional arguments¶

General option¶

-h, --help¶: show the help message and exit

Scaffolding option¶

--back ORGASM:BACK¶: The number of bases taken at the end of contigs to jump with paired-ends [default: <estimated>]