improve organisation of README

README.md

@@ -1,42 +1,42 @@
-Download genomes used for mOTUs 3
+Download  mOTUs 3 genomes
 ========
 
-This tool downloads the 700,000 genomes used for the mOTUs 3 database.
+This tool allows to download all or any of the 700,000 genomes used for the mOTUs 3 database. The user can download a specific genome (type), all genomes associated with a specific mOTU, or the complete database.
+
+## Installation 
+To run the script, clone this repository
 
-First, clone this repository
 ```
 git clone https://github.com/motu-tool/motus_v3_genomes
 cd motus_v3_genomes
 ```
 
+## Downloading genomes
+
+The data will be downloaded into the same folder where the script is located, under a folder with the name `motus_v3_genomes`.
+
+The structure is as follows:
+- Within `motus_v3_genomes` there is a folder for each mOTU
+- Within each mOTU folder are the genomes associated with this mOTU. In addition,  there is a file `1.list_files.txt`. This file lists the paths to each of the downloaded genome files.
+- If you run `motus_genomes_download -m all`, an additional file `1.list_all_files.txt` will be created within `motus_v3_genomes`.
+
+Note that all files are first downloaded to `motus_v3_genomes/temp_dir` and moved to the final destination once the download and unzip are complete.
+
+The script automatically checks the md5 sum of each of the downloaded files.
+
+
 To download one genome type (for example the MAG `LIAN20-1_SAMN11649416_METAG_000035`):
+
 ```
 python motus_genomes_download -m LIAN20-1_SAMN11649416_METAG_000035
 ```
 
-To download all genomes from one motu (for example the ref mOTU `ref_mOTU_v3_00006`):
+To download all genomes from one mOTU (for example the ref mOTU `ref_mOTU_v3_00006`):
 ```
 python motus_genomes_download -m ref_mOTU_v3_00006
 ```
 
-To download all genomes:
-```
-python motus_genomes_download -m all
-```
-
-
-
-The script automatically checks the md5 sum of the downloaded file.
-
-The data will be downloaded in the same folder where the script is located, under a folder with the name `motus_v3_genomes`.
-The structure is as follows:
-- Within `motus_v3_genomes` there is a folder per mOTU
-- Within each mOTU folder there is a file `1.list_files.txt` with the path to the files, and the files of the genomes are within the mOTU directory
-- If you run `motus_genomes_download -m all` an additional file `1.list_all_files.txt` will be created within `motus_v3_genomes`.
-
-Note that all files are first downloaded to `motus_v3_genomes/temp_dir` and moved to the final destination once the download and unzip is complete.
-
-If you run the two commands listed above to download a genome and mOTU, you will end up with the following structure:
+If you run the two commands above to download a genome and mOTU, you will end up with the following structure:
 ```
 .
 |-- README.md
@@ -54,7 +54,12 @@ If you run the two commands listed above to download a genome and mOTU, you will
     `-- temp_dir
 ```
 
-Finally, you can list all motus and the number of associated genomes (available for download) with:
+To download all genomes:
+```
+python motus_genomes_download -m all
+```
+
+Finally, you can list all mOTUs and the number of associated genomes (available for download) with:
 ```
 python motus_genomes_download -l
 ```