A thread is a unit of execution on your processor. Using multithreading can increase execution speed of the job. Set it as high as you want, depends on the number of available threads. On Linux the command nproc tells you how many you have. The speed increase is not linear though since at some point you are restricted by I/O bottlenecks.
From the manual:
-t integer Number of threads to use. The default value of 0 is configured to automatically use up to 4 CPU cores (if present). Numbers higher than 4 (or maybe 8) will probably not make much sense because of diminishing returns.
So I would start with 4 if your machine supports that.
As a remark, please be sure to not open a question for every parameter of MIRA you have a questions about, leave it in this thread and use ADD COMMENT. We will close further threads unless they are fundamentally different from this one here. This is not meant to be impolite put intends to keep content focused in a single post thread rather than being split over multiple ones.
Question about Mira parameters
Mira assembler with IonTorrent
Guys, it's me again.
I performed an execution in MIRA and the log returned the following message:
"Out of memory detected, exception message is: std :: bad_alloc"
Is this due to my machine's lack of processing power?
What are you machine specs? MIRA is very resource hungry, and excess sequencing coverage can cause an explosion of memory consumption. The manual recommends down-sampling to ~100x coverage.
My machine has a seventh generation Intel Core i7 processor and dedicated 2GB video memory.
The Log file did not indicate coverage problems with the readings, but identified chimeric read in the file.