WARNING: not all combinations of the following options have been tested, please use them carefully and avoid conflicting parameters and values. We do not guarantee consistency of unexpected combinations of parameters.
Filters for primer-like features (see here for details)
-e [ --min-ending-GC ] arg (=60) set the minimum percentage of Cs and Gs in the last 5 nucleotides ([0, 100], default: 60) (see section
1.3.2 on Suppl. File S1)
-g [ --min-GC ] arg (=40) set the minimum percentage of Cs and Gs in retrieved words ([0, 100], default: 40) (see section
1.3.1 on Suppl. File S1)
-G [ --max-GC ] arg (=60) set the maximum percentage of Cs and Gs in retrieved words ([0, 100], default: 60) (see section
1.3.1 on Suppl. File S1)
-H [ --homopolymers ] arg (=5) set the maximum length of allowed homopolymers ([0, w], default: 5) (see section
1.3.3 on Suppl. File S1)
-m [ --min-melting-temp ] arg (=50) set the minimum allowed melting temperature ([0, 100], default: 50) (see section
1.3.6 on Suppl. File S1)
-M [ --max-melting-temp ] arg (=60) set the maximum allowed melting temperature ([0, 100], default: 60) (see section
1.3.6 on Suppl. File S1)
-P [ --palin-sub-seq ] arg (=8) set the maximum allowed size for palindrome sub-sequences ([0, w], default: 8) (see section
1.3.4 on Suppl. File S1)
-S [ --self-dimers ] arg (=3) set the maximum length of allowed self-dimers ([0, w], default: 3) (see section
1.3.4 on Suppl. File S1)
-b [ --threads-per-block ] arg (=256) GPU setting, number of threads per block ([2, 512], default: 256)
-B [ --max-blocks-per-grid ] arg (=64) GPU setting, maximum number of blocks per grid ([2, 2048], default: 64)
-k [ --sequences-per-kernel ] arg (=8) GPU setting, number of sequence pairs processed in each kernel invocation ([2, 2e9], default: 8)
-C [ --cuda-memory ] arg (=0)
select the CUDA memory type: 0 for normal, 1 for pinned, 2 for (pinned) zero-copy, default: 0
* -n [ --num-threads ] arg (=0) set the number of concurrent CPU threads to use, 0 for automatic ([0, 32], default: 0)
