From dfd7720f5a3e109ce556cdd17c02c023d91d8db0 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 17 Apr 2021 16:28:12 -0400
Subject: [PATCH] clarify that hifiasm doesn't do scaffolding

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 4702cfa..d7318c1 100644
--- a/README.md
+++ b/README.md
@@ -119,6 +119,9 @@ challenging. Users should not expect hifiasm to phase entire chromosomes at the
 moment. Also, contigs from different parental chromosomes are randomly mixed as
 it is just not possible to phase across chromosomes with Hi-C.
 
+Hifiasm does not perform scaffolding for now. You need to run a standalone
+scaffolder such as SALSA or 3D-DNA to scaffold phased haplotigs.
+
 ### <a name="trio"></a>Trio binning
 
 When parental short reads are available, hifiasm can also generate a pair of