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 root filename (produced by the oa index command)


output prefix

optional arguments

General option

-h, --help

show the help message and exit

Scaffolding option


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