From 178b896bbbba5ae1d6aaa7d7443797884029d071 Mon Sep 17 00:00:00 2001
From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com>
Date: Wed, 14 Aug 2024 11:45:20 +0900
Subject: [PATCH 1/2] Update README.md

remove deprecated options
---
 README.md | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/README.md b/README.md
index e9153ba0..e33bf355 100644
--- a/README.md
+++ b/README.md
@@ -113,8 +113,6 @@ metabuli classify --seq-mode 3 read.fna dbdir outdir jobid
    --min-score : The minimum score to be classified 
    --min-sp-score : The minimum score to be classified at or below species rank. 
    --taxonomy-path: Directory where the taxonomy dump files are stored. (DBDIR/taxonomy by default)
-   --reduced-aa : 0. Use 20 alphabets or 1. Use 15 alphabets to encode amino acids. 
-                  Give the same value used for DB creation.
    --accession-level : Set 1 to use accession level classification (0 by default). 
                        It is available when the DB is also built with accession level taxonomy.
 ```
@@ -217,10 +215,8 @@ metabuli build <DBDIR> <LIB_FILES> <accession2taxid> [options]
 - accession2taxid : A path to NCBI-style accession2taxid.
   
   * Options
-   --threads : The number of CPU-cores used (all by default)
+   --threads : The number of threads used (all by default)
    --taxonomy-path: Directory where the taxonomy dump files are stored. (DBDIR/taxonomy by default)
-   --reduced-aa : 0. Use 20 alphabets or 1. Use 15 alphabets to encode amino acids.
-   --spacing-mask : Binary mask for spaced metamer. The same mask must be used for DB creation and classification. A mask should contain at least eight '1's, and '0' means skip.
    --accession-level : Set 1 to use accession level taxonomy (0 by default).
 ```
 This will generate **diffIdx**, **info**, **split**, and **taxID_list** and some other files. You can delete '\*\_diffIdx' and '\*\_info' if generated.

From ed609df8d5f59987fc4cd53eaebba3741fd890d7 Mon Sep 17 00:00:00 2001
From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com>
Date: Wed, 14 Aug 2024 14:57:33 +0900
Subject: [PATCH 2/2] Update README.md

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

diff --git a/README.md b/README.md
index e33bf355..45b0ad89 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,7 @@ Please cite: [Kim J, Steinegger M. Metabuli: sensitive and specific metagenomic
 
 ## Update in v1.0.6
 - Windows OS is supported.
+> We found Metabuli is too slow with Windows OS. Currently making it faster.
 
 ## Update in v1.0.4
 - Fixed a minor reproducibility issue.