specifically mention guppy5 supper accuracy

krol33 · Sep 5, 2021 · 9c975dd · 9c975dd
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diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@ Latest updates
 
 ### Flye 2.9 release (20 Aug 2022)
 * Better assembly of very short sequences (e.g. plasmids or viruses). They vere often missed in previous versions.
-* New --nano-hq mode for ONT Guppy5+ and Q20 reads (3-5% error rate)
+* New --nano-hq mode for ONT Guppy5+ (SUP mode) and Q20 reads (3-5% error rate)
 * Optimized default parameters for HiFi (HPC error threshold 0.01 -> 0.001; increased min overlap)
 * Polishing improvements: reduced number of possible clusters of errors
 * Improvements in repeat detection algorithm to further limit a chance of (otherwise infrequent) misassemblies

diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -50,7 +50,7 @@ Are PacBio CCS/HiFi reads supported?
 
 Yes, use the `--pacbio-hifi` option. 
 
-Are there any special parameters/modes for the newest ONT data (Guppy 5+, Q20)?
+Are there any special parameters/modes for the newest ONT data (Guppy 5+ SUP, Q20)?
 -------------------------------------------------------------------------------
 
 Yes, use the new `--nano-hq` mode.

diff --git a/docs/NEWS.md b/docs/NEWS.md
@@ -1,7 +1,7 @@
 Flye 2.9 release (20 Aug 2022)
 =============================
 * Better assembly of very short sequences (e.g. plasmids or viruses). They vere often missed in previous versions.
-* New --nano-hq mode for ONT Guppy5+ and Q20 reads (3-5% error rate)
+* New --nano-hq mode for ONT Guppy5+ SUP and Q20 reads (3-5% error rate)
 * Optimized default parameters for HiFi (HPC error threshold 0.01 -> 0.001; increased min overlap)
 * Polishing improvements: reduced number of possible clusters of errors
 * Improvements in repeat delection algorithm to further limit a chance of (otherwise infrequent) misassemblies

diff --git a/docs/USAGE.md b/docs/USAGE.md
@@ -42,7 +42,7 @@ optional arguments:
   --nano-corr path [path ...]
                         ONT reads that were corrected with other methods (<3% error)
   --nano-hq path [path ...]
-                        ONT high-quality reads: Guppy5+ or Q20 (<5% error)
+                        ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error)
   --subassemblies path [path ...]
                         [deprecated] high-quality contigs input
   -g size, --genome-size size
@@ -125,7 +125,7 @@ The dataset was originally released by the
 range of datasets, from old R7 pores to the most recent R9.x and R10.x. The
 expected error rate is 10-15%.
 
-* For the most recent ONT data basecalled with Guppy5 use the new `--nano-hq` mode.
+* For the most recent ONT data basecalled with Guppy5+ SUP use the new `--nano-hq` mode.
 Expected error rate is <5%.
 
 * For Q20 data, use a combination of `--nano-hq` and `--read-error 0.03`.

diff --git a/flye/main.py b/flye/main.py
@@ -687,7 +687,7 @@ def check_int_range(value, min_val, max_val, require_odd=False):
                         help="ONT reads that were corrected with other methods (<3%% error)")
     read_group.add_argument("--nano-hq", dest="nano_hq", nargs="+",
                         default=None, metavar="path",
-                        help="ONT high-quality reads: Guppy5+ or Q20 (<5%% error)")
+                        help="ONT high-quality reads: Guppy5+ SUP or Q20 (<5%% error)")
     read_group.add_argument("--subassemblies", dest="subassemblies", nargs="+",
                         default=None, metavar="path",
                         help="[deprecated] high-quality contigs input")