How to use minimap2?

Question

[MobiusT]

Hi, I am new to bioinformatics and I am tasked to do a read alignment. I have fastq.gz files, and I should run minimap2 over those datasets, which are long reads from Oxford nanopore. In the manual sent me, minimap2 [-x $preset] -d reference_index.mmi reference.fa and minimap2 -ax map-ont [-t $threads] reference_index.mmi ont_reads.fq > output.sam is said to be run over dataset. I understood that first one is creating minimizer index and second for mapping. How does .mmi represent here and how can use fast.gz files for read mapping(lets assume I have file dataset.fastq.gz)? Should I run these two command consequtively?

Answer 1

[GenoMax]

Correct. You create index in step 1 and the align your data in step 2. Two command above represent these two steps.

How does .mmi represent here

That is the index file created from reference.fa.