This adds three additional parameters to brownie:
--visits limits the number of nodes that can be visited in a single bubble detection (stage 4) [default = 1000]
--depth limits the read alignment recursion (stage 5) [default = 1000]
--essa changes the sparseness factor of essaMEM, reducing memory usage [default = 1]
The default values are identical to the values that were hardcoded before these changes were made.
It should be noted that essaMEM does not always find all MEMs when the sparseness factor is larger than 1. This has yet to be fixed. For now, this option allows brownie to run with lower memory usage, but with a possible drop in read correction performance.
This adds three additional parameters to brownie: --visits limits the number of nodes that can be visited in a single bubble detection (stage 4) [default = 1000] --depth limits the read alignment recursion (stage 5) [default = 1000] --essa changes the sparseness factor of essaMEM, reducing memory usage [default = 1] The default values are identical to the values that were hardcoded before these changes were made.
It should be noted that essaMEM does not always find all MEMs when the sparseness factor is larger than 1. This has yet to be fixed. For now, this option allows brownie to run with lower memory usage, but with a possible drop in read correction performance.