From 33fb1c785191ce69d1717c93f311373ae95d8c46 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Fri, 9 Dec 2022 10:24:10 -0600
Subject: [PATCH] fix the README and the documentation

---
 README.md                 |  2 +-
 docs/rst/installation.rst | 14 ++++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 53e64b8..87843d7 100644
--- a/README.md
+++ b/README.md
@@ -264,7 +264,7 @@ This means that the docker image can run on processors that support AVX or later
 To achieve better performance, it is **STRONGLY RECOMMENDED** to build the docker image locally after replacing `-march=sandybridge` with `-march=native` and the `Generic` build type with `Release` in the `Dockerfile`:
 
 ```bash
-sed -i 's/-march=haswell/-march=native/g' Dockerfile 
+sed -i 's/-march=sandybridge/-march=native/g' Dockerfile 
 sed -i 's/Generic/Release/g' Dockerfile 
 ```
 
diff --git a/docs/rst/installation.rst b/docs/rst/installation.rst
index 4cd023c..7c833d1 100644
--- a/docs/rst/installation.rst
+++ b/docs/rst/installation.rst
@@ -70,14 +70,16 @@ build docker locally
 --------------------------
 
 Multiple ``pggb``'s tools use SIMD instructions that require AVX (like ``abPOA``) or need it to improve performance.
-The currently built docker image has ``-march=haswell`` set.
-This means that the docker image can run on processors that support AVX256 or later, improving portability, but preventing your system hardware from being fully exploited.
+The currently built docker image has ``-Ofast -march=sandybridge`` set.
+This means that the docker image can run on processors that support AVX or later, improving portability, but preventing your system hardware from being fully exploited.
+In practice, this could mean that specific tools are up to 9 times slower.
+And that a pipeline runs ~30% slower compared to when using a native build docker image.
 
-To achieve better performance, it is **STRONGLY RECOMMENDED** to build the docker image locally after replacing ``-march=haswell`` with ``-march=native`` and the ``Generic` build type with `Release`` in the ``Dockerfile``:
+To achieve better performance, it is **STRONGLY RECOMMENDED** to build the docker image locally after replacing ``-march=sandybridge`` with ``-march=native`` and the ``Generic` build type with `Release`` in the ``Dockerfile``:
 
 .. code-block:: bash
 
-    sed -i 's/-march=haswell/-march=native/g' Dockerfile
+    sed -i 's/-march=sandybridge/-march=native/g' Dockerfile
     sed -i 's/Generic/Release/g' Dockerfile
 
 To build a docker image locally using the ``Dockerfile``, execute:
@@ -93,6 +95,8 @@ Staying in the ``pggb`` directory, we can run ``pggb`` with the locally build im
 
     docker run -it -v ${PWD}/data/:/data ${USER}/pggb "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -C cons,100,1000,10000 -m"
 
+A script that handles the whole building process automatically can be found at `https://github.com/nf-core/pangenome#building-a-native-container <https://github.com/nf-core/pangenome#building-a-native-container>`_`.
+
 
 Singularity
 ======
@@ -122,6 +126,8 @@ For Singularity to be able to read and write files to a directory on the host op
 .. code-block:: bash
     singularity run -B ${PWD}/data:/data ../pggb_latest.sif "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m"
 
+A script that handles the whole building process automatically can be found at `https://github.com/nf-core/pangenome#building-a-native-container <https://github.com/nf-core/pangenome#building-a-native-container>`_`.
+
 
 Bioconda
 ========