I wonder if anyone could recommend parameters they have used/may think
beneficial for creating a genome index?
My genome of interest is approximately the same size as that of the human
genome. The size of the fragments I wish to align to the genome are
generally much longer than examples given in the relevant literature:
Mean sequence length: 305.87 ± 115.85 bp
Minimum length: 1 bp
Maximum length: 796 bp
Length range: 796 bp
Mode length: 381 bp with 2,482 sequences
So far I have the following possible parameters to suit my data set.
Key size =22
Hash width = 14
K cals = 8
Also, with just 1 index do I need only 1 mask?
If so could anyone recommend a mask they have deemed efficient in human size
genomes with a similar read length distribution?
Any pointers would be much appreciated.