Hi can you simply provide a command that will give the lowest memory usage? I just want a simple/basic "no thrills" assembly (it will be used as input for another program)! it is not clear the impact of all the parameters on memory consumption, nor do I have time to test. So how would you modify the following parameters for low memory consumption, lets say for a an average 150PE dataset:
and please ignore the fact I have -m set to 120gb, that is just for testing. All I want to know is what parameters would give the lowest memory consumption for an assembly?
Hi can you simply provide a command that will give the lowest memory usage? I just want a simple/basic "no thrills" assembly (it will be used as input for another program)! it is not clear the impact of all the parameters on memory consumption, nor do I have time to test. So how would you modify the following parameters for low memory consumption, lets say for a an average 150PE dataset:
megahit -1 MERGED_R1_val_1.fq.gz -2 MERGED_R2_val_2.fq.gz --k-list 59,79,99,119,141 --no-mercy --bubble-level 0 --prune-level 3 --prune-depth 5 --cleaning-rounds 3 --no-local --kmin-1pass --no-hw-accel --continue -t 1 -m 120e9 --mem-flag 0 -o Megahit_OUT --min-contig-len 500
regards
and please ignore the fact I have -m set to 120gb, that is just for testing. All I want to know is what parameters would give the lowest memory consumption for an assembly?