diff jbrowse2.xml @ 5:efc64d8f4b72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9

--- a/jbrowse2.xml	Tue Jan 09 02:37:42 2024 +0000
+++ b/jbrowse2.xml	Tue Jan 09 05:24:48 2024 +0000
@@ -997,8 +997,6 @@
 can be used to let your users understand relationships between large
 groups of tracks.
 
-.. image:: sections.png
-
 Annotation Tracks
 -----------------
 
@@ -1011,6 +1009,11 @@
 These are standard feature tracks. They usually highlight genes,
 mRNAs and other features of interest along a genomic region.
 
+When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
+to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
+selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
+well for relatively sparse bed files.
+
 BAM Pileups
 ~~~~~~~~~~~
 
@@ -1021,8 +1024,6 @@
 BlastXML
 ~~~~~~~~
 
-.. image:: blast.png
-
 JiG now supports both blastn and blastp datasets. JiG internally uses a
 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
 format amenable to visualization in JBrowse. This tool is also
@@ -1044,12 +1045,6 @@
 **Protein blast search** option merely informs underlying tools that
 they should adjust feature locations by 3x.
 
-Bigwig XY
-~~~~~~~~~
-
-.. image:: bigwig.png
-
-
 
 VCFs/SNPs
 ~~~~~~~~~