Merge branch 'aligner_docs_update' into 'master'

aligner: updated the docs to reflect the new default lr:hq parameters

See merge request machine-learning/dorado!974

README.md

@@ -191,7 +191,7 @@ To basecall with alignment with duplex or simplex, run with the `--reference` op
 $ dorado basecaller <model> <reads> --reference <index> > calls.bam
 ```
 
-Alignment uses [minimap2](https://github.com/lh3/minimap2) and by default uses the `map-ont` preset. This can be overridden with the `-k` and `-w` options to set kmer and window size respectively.
+Alignment uses [minimap2](https://github.com/lh3/minimap2) and by default uses the `lr:hq` preset. This can be overridden with the `--mm2-preset` option or using `-k` and `-w` options to set kmer and window size respectively.
 
 ### Sequencing Summary
 

dorado/cli/aligner.cpp

@@ -84,7 +84,7 @@ int aligner(int argc, char* argv[]) {
     cli::ArgParser parser("dorado aligner");
     parser.visible.add_description(
             "Alignment using minimap2. The outputs are expected to be equivalent to minimap2.\n"
-            "The default parameters use the map-ont preset.\n"
+            "The default parameters use the lr:hq preset.\n"
             "NOTE: Not all arguments from minimap2 are currently available. Additionally, "
             "parameter names are not finalized and may change.");
     parser.visible.add_argument("index").help("reference in (fastq/fasta/mmi).");