Minimap2: choosing k-mer length and index size during indexing

[sandipmkale]

Hello,
I have a very big genome of 15G size and would like to use it for mapping 150 bp PE reads. I wanted to index it before.
when I used -k 31 and -I 50G, I got following error:
minimap2: sketch.c:84: mm_sketch: Assertion `len > 0 && (w > 0 && w < 256) && (k > 0 && k <= 28)' failed.
Aborted
Please help to select optimum parameters.

Thanks and regards

Sandip

[tseemann]

The error says that only k values up to 28 are supported.
The --help also says -k INT k-mer size (no larger than 28) [15]
Try -k 28 ?

Also, @lh3 says that bwa mem is still the better choice for aligning 150bp PE Illumina/MGI reads.

[lh3]

As @tseemann said (thank you!)