Minimap2 map-pb index for ONT reads

Question

[compuTE]

Hi!

I made a minimap2 index for a custom genome. I was planning on using it for pacbio and nanopore data.

I created the index using minimap2 -x map-pb -d genome.mmi genome.fa. Unfortunately, I forgot to make one specifically for the nanopore data using map-ont... Instead, I mapped both data sets to the same index using

For the nanopore: minimap2 -a -x map-ont genome.mmi sample.fastq.gz

For the pacbio: minimap2 -a -x map-pb genome.mmi sample.fastq.gz

I have limited experience with minimap2 and I am wondering if this is a big deal, since the mapping was using the correct parameters - it's just the index that might not be perfect for the data...

Can someone explain to me how this could affect the performance? If it would? I can't seem to find a thorough explanation about this.

Thanks,

[GenoMax]

compuTE : If you can provide an update in this thread with some stats (samtools idxstats may be good enough) as to how the numbers change with a common index used for ONT and PacBio VS specific indexes made for the two datasets.

minimap2 is such an excellent aligner that the gross stats may remain very similar (specifics may change some).

Rarely do people have both types of data and this insight would provide a very useful datapoint.

Answer 1

[biofalconch]

Directly from the minimap2 page

Importantly, it should be noted that once you build the index, indexing parameters such as -k, -w, -H and -I can't be changed during mapping. If you are running minimap2 for different data types, you will probably need to keep multiple indexes generated with different parameters. This makes minimap2 different from BWA which always uses the same index regardless of query data types.

So the answer is yes, I don't know how these parameters change between data types but I wouldn't assume they would work interchangeably without any benchmarking.

[compuTE]

Ok, good to know. Thank you for pointing to it. I'll redo and compare the index and bam stats - I'll update about it then.

Answer 2

[colindaven]

Why build an index at all? I never build indices for minimap2 mapping, unless forced to by a further tool eg megalodon. Then I can set the mapping type using appropriately using -x map-ont or map-pb as appropriate.