usage: bogart -o outputName -O ovlStore -G gkpStore -T tigStore
-O Mandatory path to an ovlStore.
-G Mandatory path to a gkpStore.
-T Mandatory path to a tigStore (can exist or not).
-o prefix Mandatory name for the output files
-B b Target number of fragments per tigStore (consensus) partition
Algorithm Options
-gs Genome size in bases.
-J Join promiscuous unitigs using unused best edges.
-SR Shatter repeats, don't rebuild.
-R Shatter repeats (-SR), then rebuild them
-RL len Force reads below 'len' bases to be singletons.
This WILL cause CGW to fail; diagnostic only.
-threads N Use N compute threads during repeat detection.
0 - use OpenMP default (default)
1 - use one thread
Overlap Selection - an overlap will be considered for use in a unitig under
the following conditions:
When constructing the Best Overlap Graph and Promiscuous Unitigs ('g'raph):
-eg 0.020 no more than 0.020 fraction (2.0%) error ** DEPRECATED **
When loading overlaps, an inflated maximum (to allow reruns with different error rates):
-eM 0.05 no more than 0.05 fraction (5.0%) error in any overlap loaded into bogart
the maximum used will ALWAYS be at least the maximum of the four error rates
For all, the lower limit on overlap length
-el 500 no shorter than 40 bases
Overlap Storage
-M gb Use at most 'gb' gigabytes of memory for storing overlaps.
-N num Load at most 'num' overlaps per read.
-create Only create the overlap graph, save to disk and quit.
-save Save the overlap graph to disk, and continue.
Debugging and Logging
-D <name> enable logging/debugging for a specific component.
-d <name> disable logging/debugging for a specific component.
overlapScoring
allBestEdges
chunkGraph
buildUnitig
placeUnplaced
bubbles
splitDiscontinuous
intermediateUnitigs
setParentAndHang
stderr
No output prefix name (-o option) supplied.
No gatekeeper store (-G option) supplied.
No overlap store (-O option) supplied.
No output tigStore (-T option) supplied.