s-andrews · ewels · Aug 12, 2025 · Aug 12, 2025 · Aug 23, 2025 · Aug 23, 2025
diff --git a/Help/3 Analysis Modules/1 Basic Statistics.html b/Help/3 Analysis Modules/1 Basic Statistics.html
@@ -1,18 +1,18 @@
 <html>
 
 <head>
-<title>Basic Statistics</title>
+<title>Basic statistics</title>
 <style type="text/css">
 	body {
 		font-family: sans-serif;
 	}
 </style>
 </head>
 <body>
-<h1>Basic Statistics</h1>
+<h1>Basic statistics</h1>
 <h2>Summary</h2>
 <p>
-The Basic Statistics module generates some simple composition
+The Basic statistics module generates some simple composition
 statistics for the file analysed.
 </p>
 
@@ -21,8 +21,8 @@ <h2>Summary</h2>
 <li>File type: Says whether the file appeared to contain actual base calls or
 colorspace data which had to be converted to base calls</li>
 <li>Encoding: Says which ASCII encoding of quality values was found in this
-file.
-</li><li>Total Sequences: A count of the total number of sequences processed.
+file.</li>
+<li>Total Sequences: A count of the total number of sequences processed.
 There are two values reported, actual and estimated.  At the moment these
 will always be the same.  In the future it may be possible to analyse just
 a subset of sequences and estimate the total number, to speed up the analysis,
@@ -41,12 +41,12 @@ <h2>Summary</h2>
 
 <h2>Warning</h2>
 <p>
-Basic Statistics never raises a warning.
+Basic statistics never raises a warning.
 </p>
 
 <h2>Failure</h2>
 <p>
-Basic Statistics never raises an error.
+Basic statistics never raises an error.
 </p>
 
 <h2>Common reasons for warnings</h2>

diff --git a/Help/3 Analysis Modules/10 Adapter Content.html b/Help/3 Analysis Modules/10 Adapter Content.html
@@ -1,15 +1,15 @@
 <html>
 
 <head>
-<title>Adapter Content</title>
+<title>Adapter content</title>
 <style type="text/css">
 	body {
 		font-family: sans-serif;
 	}
 </style>
 </head>
 <body>
-<h1>Adapter Content</h1>
+<h1>Adapter content</h1>
 <h2>Summary</h2>
 <p>
 The Kmer Content module will do a generic analysis of all of the Kmers

diff --git a/Help/3 Analysis Modules/4 Per Base Sequence Content.html b/Help/3 Analysis Modules/4 Per Base Sequence Content.html
@@ -59,15 +59,15 @@ <h2>Common reasons for warnings</h2>
 <ol>
 <li>Overrepresented sequences: If there is any evidence of overrepresented
 sequences such as adapter dimers or rRNA in a sample then these sequences 
-may bias the overall composition and their sequence will emerge from this plot.
+may bias the overall composition and their sequence will emerge from this plot.</li>
 <li>Biased fragmentation: Any library which is generated based on the ligation
 of random hexamers or through tagmentation should theoretically have good
 diversity through the sequence, but experience has shown that these libraries 
 always have a selection bias in around the first 12bp of each run.  This is
 due to a biased selection of random primers, but doesn't represent any individually
 biased sequences.  Nearly all RNA-Seq libraries will fail this module because of
 this bias, but this is not a problem which can be fixed by processing, and it 
-doesn't seem to adversely affect the ablity to measure expression.
+doesn't seem to adversely affect the ablity to measure expression.</li>
 <li>Biased composition libraries: Some libraries are inherently biased in their
 sequence composition.  The most obvious example would be a library which has been 
 treated with sodium bisulphite which will then have converted most of the cytosines
@@ -80,6 +80,7 @@ <h2>Common reasons for warnings</h2>
 only sequences which do not match.  Sudden deviations in composition at the end
 of libraries which have undergone aggressive trimming are therefore likely to be
 spurious.</li>
+</ol>
 
 </body>
 </html>
diff --git a/Help/3 Analysis Modules/6 Per Base N Content.html b/Help/3 Analysis Modules/6 Per Base N Content.html
@@ -13,7 +13,7 @@ <h1>Per Base N Content</h1>
 <h2>Summary</h2>
 <p>
 If a sequencer is unable to make a base call with sufficient confidence
-then it will normally substitute an N rather than a conventional base]
+then it will normally substitute an N rather than a conventional base
 call
 </p>
 <p>

diff --git a/Help/3 Analysis Modules/7 Sequence Length Distribution.html b/Help/3 Analysis Modules/7 Sequence Length Distribution.html
@@ -1,15 +1,15 @@
 <html>
 
 <head>
-<title>Sequence Length Distribution</title>
+<title>Sequence length distribution</title>
 <style type="text/css">
 	body {
 		font-family: sans-serif;
 	}
 </style>
 </head>
 <body>
-<h1>Sequence Length Distribution</h1>
+<h1>Sequence length distribution</h1>
 <h2>Summary</h2>
 <p>
 Some high throughput sequencers generate sequence fragments

diff --git a/README.md b/README.md
@@ -1,4 +1,10 @@
-# FastQC
+<h1>
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="uk/ac/babraham/FastQC/Resources/fastqc_logo_darkbg.svg">
+  <source media="(prefers-color-scheme: light)" srcset="uk/ac/babraham/FastQC/Resources/fastqc_logo.svg">
+  <img src="uk/ac/babraham/FastQC/Resources/fastqc_logo.svg" alt="FastQC">
+</picture>
+</h1>
 
 **A Quality Control application for FastQ files**
 
@@ -23,16 +29,24 @@ FastQC is an application which takes a FastQ file and runs a series of tests on
 FastQC can be run either as an interactive graphical application which allows you to view results for multiple files in a single application.  Alternatively you can run the program in a non interactive way (say as part of a pipeline) which will generate an HTML report for each file you process.
 
 FastQC is a cross-platform application, written in java. In theory it should run on any platform which has a suitable java runtime environment.
-Having said that we've only tested in on Windows, MacOSX and Linux running the Oracle v1.6 to 1.8 JREs.  Please let us know what happened if you try running it on other platforms / JREs.  Please see the detailed instructions in the INSTALL.txt document to tell you how to get a suitable java version to run FastQC on your system.
+Having said that we've only tested in on Windows, MacOSX and Linux running the Oracle v1.6 to 1.8 JREs.  Please let us know what happened if you try running it on other platforms / JREs.
+Please see the detailed instructions [in `INSTALL.md`](`INSTALL.md`) to tell you how to get a suitable java version to run FastQC on your system.
 
 ## Installation
 
 Please see the [**project web page**](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the [installation instructions](INSTALL.md) in this repository.
 
 ## Contributions
 
-If you have any comments about FastQC we would like to hear them.  You can either enter them into the github bug tracker at:
+If you have any comments about FastQC we would like to hear them.
+You can either create a [GitHub issue](https://github.com/s-andrews/FastQC/issues/) or send them directly to simon.andrews@babraham.ac.uk.
 
-https://github.com/s-andrews/FastQC/issues/
+FastQC was written by Simon Andrews, at the Babraham Institute, Cambridge, UK.
 
-..or send them directly to simon.andrews@babraham.ac.uk.
+https://www.bioinformatics.babraham.ac.uk/
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="uk/ac/babraham/FastQC/Resources/babraham_darkbg.svg">
+  <source media="(prefers-color-scheme: light)" srcset="uk/ac/babraham/FastQC/Resources/babraham.svg">
+  <img src="uk/ac/babraham/FastQC/Resources/babraham.svg" alt="Babraham Institute" width=100>
+</picture>
diff --git a/Templates/Icons/error.png b/Templates/Icons/error.png
diff --git a/Templates/Icons/error.svg b/Templates/Icons/error.svg
diff --git a/Templates/Icons/fastqc_icon.png b/Templates/Icons/fastqc_icon.png
diff --git a/Templates/Icons/fastqc_icon.svg b/Templates/Icons/fastqc_icon.svg
diff --git a/Templates/Icons/pass.svg b/Templates/Icons/pass.svg
diff --git a/Templates/Icons/tick.png b/Templates/Icons/tick.png
diff --git a/Templates/Icons/warning.png b/Templates/Icons/warning.png
diff --git a/Templates/Icons/warning.svg b/Templates/Icons/warning.svg