Docs: changes, manual and version for 5.1.0.rc1

Author: alexeigurevich

CHANGES.txt

@@ -24,22 +24,20 @@
          a contig if it covers more than 95% of a cyclic chromosome/plasmid (prokaryotes only).
 
       4. Small fixes (rare crashes or slightly incorrect results in specific cases):
-       - GC calculation;
-       - duplication ratio calculation in case of Ns stretches in misassembled contigs;
-       - HTML report heatmap colors for partial BUSCO genes;
-       - use of provided BAM files;
-       - problems with ?
-
-      5. Cosmetic changes in warning/notice/error messages, pipeline steps order, etc.
+       - GC calculation (zero division due to rate side effects);
+       - duplication ratio (fractional overestimation due to Ns stretches in some contigs);
+       - HTML report heatmap colors for partial BUSCO genes (red-blue color switch);
+       - use of provided BAM files (--bam option not working properly);
+       - postprocessing of minimap2 mediocre aligments (good pairs of alignments with a
+         strecth of mismatches/indels/Ns in between were skipped due to low averageg IDY).
+
+      5. Updates in embedded tools:
+       - new version of SILVA database (138);
+       - fixed links to BUSCO databases (v3/odb9);
+       - new GeneMark license files.
 
-      PLANNED TO BE INCLUDED IN 5.1.0:
-      x. New metrics:
-       - auNx, auNAx, auNGx, auNGAx (area under Nx, NGx, etc curves).
+      6. Cosmetic changes in warning/notice/error messages, pipeline steps order, etc.
 
-      x. Updates in embedded tools:
-       - new version of SILVA database (now: 132);
-       - new versions of BUSCO databases;
-       - new GeneMark license files.
 
 5.0.2
       1. Fixed bug with missing genome features reference stats and plot in report.html

VERSION.txt

@@ -1 +1 @@
-5.1.0.dev0
+5.1.0rc1

manual.html

@@ -102,7 +102,7 @@ <h1>QUAST 5.1.0 manual</h1>
     for guidelines on how to complete the licensing process.
     <br>
     <br>
-    Version 5.1.0 of QUAST was released under GPL v2 on April XX, 2020. Note that some of build-in third-party tools are not under GPL v2. See <a href="LICENSE.txt">LICENSE</a> for details.
+    Version 5.1.0rc1 (release candidate) of QUAST was released under GPL v2 on April 29, 2020. Note that some of build-in third-party tools are not under GPL v2. See <a href="LICENSE.txt">LICENSE</a> for details.
 </p>
 
 <h2>Contents</h2>
@@ -176,12 +176,20 @@ <h2>1. Installation</h2>
     sudo apt-get install -y pkg-config libfreetype6-dev libpng-dev python-matplotlib
 </pre>
 <br>
+<!--
 To download the <a href="https://downloads.sourceforge.net/project/quast/quast-5.1.0.tar.gz">QUAST source code tarball</a> and extract it, type:
 <pre class="code">
     wget https://downloads.sourceforge.net/project/quast/quast-5.1.0.tar.gz
     tar -xzf quast-5.1.0.tar.gz
     cd quast-5.1.0
 </pre>
+-->
+To download the <a href="https://github.com/ablab/quast/releases/download/quast_5.1.0rc1/quast-5.1.0rc1.tar.gz">QUAST source code tarball</a> and extract it, type:
+<pre class="code">
+    wget https://github.com/ablab/quast/releases/download/quast_5.1.0.rc1/quast-5.1.0rc1.tar.gz
+    tar -xzf quast-5.1.0rc1.tar.gz
+    cd quast-5.1.0rc1
+</pre>
 
 <br>
 <p>
@@ -358,7 +366,7 @@ <h3>2.3 Command line options</h3>
 <ol class='my_ol' style='margin-top: 0;'>
 <li>For gene finding, GeneMark-ES is used with <code>--fungus</code> option.
 <li><a href='#rna_finding'>Barrnap</a> will use eukaryotic database to predict ribosomal RNA genes.
-<li>><a href='#busco'>BUSCO</a> will use fungal database to find conserved orthologs.
+<li><a href='#busco'>BUSCO</a> will use fungal database to find conserved orthologs.
 <li>By default, QUAST assumes that a genome is circular and correctly processes its linear representation.
 This options indicates that the genome is not circular.
 </ol>