update read me

README.md

@@ -4,15 +4,22 @@
 
 ---
 
-## MGIKIT 
+## MGIKIT
+
 mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.
 
 The toolkit includes the following commands:
 
+## User Guide
+
+A comprehensive documentation is available at [https://sagc-bioinformatics.github.io/mgikit/](https://sagc-bioinformatics.github.io/mgikit/)
+
 ### demultiplex
+
 This command is used to demultiplex fastq files and assign the sequencing reads to their
 associated samples. The tool requires the following mandatory input files to perform the
 demultiplexing:
+
 1. Fastq files (single/paired-end).
 2. Sample sheet which contains sample indexes and their templates (will be explained in detail).
 
@@ -25,11 +32,11 @@ as well as some summary reports that can be visualised through the MultiQC tool
 
 ### template
 
-This command is used to detect the location and form of the indexes within the read barcode. It simply goes through a small number of the reads and investigates the number of matches with the indexes in the sample sheet within each possible location in the read barcode and considering the indexes as is and their reverse complementary. 
+This command is used to detect the location and form of the indexes within the read barcode. It simply goes through a small number of the reads and investigates the number of matches with the indexes in the sample sheet within each possible location in the read barcode and considers the indexes as is and their reverse complementary.
 
-It reports matches for all possible combinations and uses the read template that had the maximum number of matches. This process happens for each sample individually and therefore, the best matching template for each sample will be reported. 
+It reports matches for all possible combinations and uses the read template that has the maximum number of matches. This process happens for each sample individually and therefore, the best matching template for each sample will be reported.
 
-Using this comprehensive scan, the tool can detect the templates for mixed libraries. 
+Using this comprehensive scan, the tool can detect the templates for mixed libraries.
 
 <hr/>
 
@@ -49,21 +56,14 @@ This command is to reformat fastq files generated by `splitBarcode` into Illumin
 
 You can use the static binary under bins directly, however, if you like to build it from the source code:
 
-You need to have Rust and cargo installed first, check rust [documenation](https://doc.rust-lang.org/cargo/getting-started/installation.html)
+You need to have Rust and Cargo installed first, check rust [documentation](https://doc.rust-lang.org/cargo/getting-started/installation.html)
 
 ```bash
 git clone https://github.com/sagc-bioinformatics/mgikit.git
 cd mgikit
 cargo build --release
 ```
 
-
-
-## User Guide
-
-Please checkout the [documeantion](https://sagc-bioinformatics.github.io/mgikit/)
-
-
 ## Commerical Use
 
 Please contact us if you want to use the software for commercial purposes.