From 81205fb34b9a0cd7fe6aa7df2624458dc97a2f87 Mon Sep 17 00:00:00 2001
From: Christina-hshi <hshi@cse.cuhk.edu.hk>
Date: Sat, 11 Apr 2020 09:31:36 -0400
Subject: [PATCH] update readme

---
 README.md | 36 +++++++++++++++++++++++++-----------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 56bd3f6..206ecad 100644
--- a/README.md
+++ b/README.md
@@ -1,31 +1,45 @@
 # SH-assembly
 SH-assembly is a bioinformatic pipeline for de novo genome assembly.
-SH-assembly is a de Bruijn-graph based method.
+It is a de Bruijn-graph based method.
 It counts the k-mers using CQF-deNoise followed by contracting unbranched paths in DBG graph to unitigs.
 The unitig graph then will be simplified using the graph simplification module in [Minia 3](https://github.com/GATB/minia).
 In the original Minia 3 program, we can not directly call its simplication module.
 Here we provide the modification upon Minia 3 (v3 git commit n3eb6f54), using which we can directly call the simplification module.
 
 ## External libraries
-- z
-- bz2
-- boost
-- tbb
+- **z**
+- **bz2**
+- **boost**
+- **tbb**
 
 ## Installation
     git clone https://github.com/Christina-hshi/SH-assembly.git
-    #in project root directory, 
+    #go to project root directory
+    cd SH-assembly
     mkdir release
     cd release
     cmake ..
-    #this will make all targets, including a customed version of CQF-deNoise, and assembly program.
-    make 
+    #this will make all targets, including a customized version of CQF-deNoise, and assembly program.
+    make
+    cd ..
+
+    #install a customized version of minia, where the simplification module can be run as an idenpendent step.
+    git clone https://github.com/Christina-hshi/Minia.git
+    cd Minia
+    git submodule init
+    git submodule update
+    mkdir release
+    cd release
+    cmake ..
+    make -j8
 
 ## User mannual
 The basic workflow of running SH-assembly is 
-    1. run "CQF-deNoise" to counting kmers
-    2. run "Contiger" to building unitig graph 
-    3. run "minia" to simplify unitig graph, and produce a list of contigs.
+
+1. run **CQF-deNoise** to counting kmers
+2. run **Contiger** to building unitig graph 
+3. run **Minia** to simplify unitig graph, and produce a list of contigs.
+
 For each program, run the program without arguments for usage instructions. 
 
 ## Contact