Phrasing

README.md

@@ -44,19 +44,21 @@ Kindel reconciles substitutions and CIGAR-described indels to to produce a major
 
 ## Installation
 
+Install inside existing Python environment:
+
 ```shell
 # Requires Python 3.8+ and Samtools
 pip install kindel
 ```
-For a complete installation using a conda-compatible package manager:
+Complete installation using a conda-compatible package manager:
 
 ```
 conda create -y -n kindel python=3.13 samtools
 conda activate kindel
 pip install kindel
 ```
 
-For a local development install:
+Development install:
 
 ```
 git clone https://github.com/bede/kindel.git
@@ -74,28 +76,20 @@ Also see [`usage.ipynb`](usage.ipynb)
 
 ### Command line
 
+Generate a consensus sequence from an aligned BAM, saving the consensus sequence to `cns.fa`:
+
 ```bash
 $ kindel consensus alignment.bam > cns.fa
 ```
-Generate a consensus sequence from an aligned BAM, saving the consensus sequence to `cns.fa`
 
 
+Generate a consensus sequence from an aligned BAM with realignment mode enabled, allowing closure of gaps in the consensus sequence:
 
 ```bash
 $ kindel consensus --realign alignment.bam > cns.fa
 ```
 
-Generate a consensus sequence from an aligned BAM with realignment mode enabled, allowing closure of small gaps in the consensus sequence
-
-
-
-```bash
-$ kindel plot alignment.bam
-```
-
-Generate an interactive plot showing aligned depth alongside insertion, deletion and soft clipping frequency across the genome
-
-
+Built in help:
 
 ```bash
 $ kindel -h
@@ -119,7 +113,7 @@ optional arguments:
   -h, --help            show this help message and exit
 
 ```
----
+
 ```bash
 $  kindel consensus -h
 usage: kindel consensus [-h] [-r] [--min-depth MIN_DEPTH]
@@ -174,18 +168,23 @@ Please let me know if you run into problems by opening a GitHub issue, tweeting
 
 ## Visualising alignments (`kindel plot`)
 
-It is useful to visualise rates of insertion, deletion and alignment clipping. `kindel plot` generates an interactive HTML plot of relevant alignment information.
+It can be useful to visualise rates of insertion, deletion and alignment clipping across an alignment. `kindel plot` generates an interactive HTML plot showing relevant alignment information.
+
+To plot aligned depth alongside insertion, deletion and soft clipping frequency:
 
 ```
 kindel plot tests/data_minimap2/2.issue23.debug.bam
 ```
+
+
 **Original alignment**
 ![Plot of original alignment](plot-before.png)
 
 **After alignment to Kindel consensus sequence**
 ![Plot after alignment to Kindel consensus sequence](plot-after.png)
 
 
+
 ## Contributing
 
 If you would like to contribute to this project, please open an issue or contact the author directly using the details above. Please note that this project is released with a [Contributor Code of Conduct](https://github.com/statsmaths/kerasR/blob/master/CONDUCT.md), and by participating in this project you agree to abide by its terms.