docs: change wording for ONT R10 data

Author: davidlougheed

README.md

@@ -114,8 +114,8 @@ long read data should still work.
   * Whole-genome and targeted genotyping modes to adjust this re-weighting.
 * Incorporation of single-nucleotide variation (SNVs) for better and faster calling plus 
   additional downstream analysis possibilities.
-  * Recommended for **HiFi data and ONT duplex data only**. In my testing, this worsens runtime and call quality for 
-    ONT ultra-long-read data, but speeds up the tool and improves call quality for HiFi/ONT duplex data. 
+  * Recommended for **HiFi data and ONT R10 data only**. In my testing, this worsens runtime and call quality for 
+    ONT ultra-long-read data, but speeds up the tool and improves call quality for HiFi/ONT R10 data. 
 * Parallelized for faster computing on clusters and for ad-hoc fast analysis of single samples.
 * 95% confidence intervals on calls via a user-configurable optional parametric bootstrapping process.
 

docs/caller_usage.md

@@ -18,12 +18,12 @@
   **Default:** 70
 * `--realign` or `-a`: Whether to perform local re-alignment to attempt recovery of soft-clipped reads. Some aligners
   may soft-clip around large insertions, e.g. with an expansion (I've noticed this with *pbmm2*/*minimap2*). 
-  Currently recommended **for HiFi or ONT duplex only**, since this step aggressively filters out realignments with many 
-  mismatches or small indels. Enabling this slows down calling, so it may not be suitable for a very large catalog of 
-  tandem repeats.
+  Currently recommended **for HiFi or ONT R10 only**, since this step aggressively filters out realignments with 
+  many mismatches or small indels. Enabling this slows down calling, so it may not be suitable for a very large catalog 
+  of tandem repeats.
 * `--hq`: Whether to treat provided reads as "high quality", i.e., fairly close to the actual true sequence. Used when 
   detecting expansions, to skip a smoothing filter that may ignore disparate, rare expansion-like read counts.
-  Use for CCS reads or similar data (e.g., duplex nanopore data) ONLY! **Default:** off
+  Use for CCS reads or similar data (e.g., R10 nanopore data) ONLY! **Default:** off
 * `--use-hp`: Whether to incorporate `HP` tags from a haplotagged alignment file. This should speed up runtime and 
   will potentially improve calling results. **This flag is experimental, and has not been tested extensively.**
 * `--incorporate-snvs [path]` or `--snv [path]`: A path to a VCF with SNVs to incorporate into the calling process and