From 1afecdcecca486f8f87e3b91658ab01d06bb03df Mon Sep 17 00:00:00 2001
From: chhylp123 <hcheng@jimmy.harvard.edu>
Date: Thu, 17 Nov 2022 12:26:33 -0500
Subject: [PATCH] update README

---
 README.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/README.md b/README.md
index 0695613..de93c52 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,7 @@ See [tutorial][tutorial] for more details.
   - [Assembling HiFi reads without additional data types](#hifionly)
   - [Hi-C integration](#hic)
   - [Trio binning](#trio)
+  - [Ultra-long ONT integration](#ul)
   - [Output files](#output)
 - [Results](#results)
 - [Getting Help](#help)
@@ -143,6 +144,14 @@ hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2> NA12878.asm.trio
 ```
 The second command line will run much faster than the first.
 
+### <a name="ul"></a>Ultra-long ONT integration
+
+Hifiasm could integrate ultra-long ONT reads to improve the assembly quality:
+```sh
+hifiasm -o NA12878.asm -t32 --ul ul.fq.gz HiFi-reads.fq.gz
+```
+Please note that this mode is not stable right now.
+
 ### <a name="output"></a>Output files
 
 Hifiasm generates different types of assemblies based on the input data.