Merge pull request #231 from wwood/fix-docs

fix dereplication docs
wwood · Dec 5, 2024 · e9938d3 · e9938d3
2 parents cb7b458 + 446e425
commit e9938d3
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diff --git a/README.md b/README.md
@@ -87,6 +87,7 @@ and some mapping software:
 * [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) v2.0
 
 For dereplication:
+* [skani](https://github.com/bluenote-1577/skani) v0.1.1
 * [Dashing](https://github.com/dnbaker/dashing) v0.4.0
 * [FastANI](https://github.com/ParBLiSS/FastANI) v1.3
 

diff --git a/src/cli.rs b/src/cli.rs
@@ -734,10 +734,10 @@ pub fn genome_full_help() -> Manual {
         Flag::new().long("--dereplicate").help(
             "Do genome dereplication via average nucleotide \
         identity (ANI) - choose a genome to represent \
-        all within a small distance, using Dashing for \
-        preclustering and FastANI for final ANI \
-        calculation. When this flag is used, dereplication occurs \
-        transparently through the Galah method (https://github.com/wwood/galah) [default: not set]",
+        all within a small distance, using skani for \
+        clustering by default. When this flag is used, \
+        dereplication occurs transparently through the \
+        Galah method (https://github.com/wwood/galah) [default: not set]",
         ),
     );
     derep_section =