Update software.md

Author: mchaisso

_pages/software.md

@@ -12,24 +12,39 @@ seg_vamos:
       STR and VNTR annotation by motif composition for PacBio and Oxford Nanopore reads, and assemblies. The vamos suite contains two components, one to characterize the repeat motifs in a population using an `efficient` motif set, a subset of motifs that preserves motif sequence diversity while removing rare motifs, and annotation software that uses wraparound dynamic programming to annotate samples using tandem repeat and motif databases.
       bioconda: vamos  
       git: https://github.com/chaissonlab/vamos
-      publication:  
+      publication:  https://link.springer.com/article/10.1186/s13059-023-03010-y
       authors: Jingwen Ren and [Bida Gu]({% link Bida_Gu.md %})  
 seg_ctyper:
   - image_path: /software/ctyperlogo.png
     title: "ctyper"
     excerpt: |
       Ctyper is a genotyping approach for pangenomes to detect alleles that are shared between a biobank (short-read sequencing) sample and a long-read pangenome for challenging and copy-number variable regions of the genome.
       bioconda: ctyper  
-      https://github.com/chaissonlab/ctyper
-
+      git: https://github.com/chaissonlab/ctyper  
+      publication: https://www.nature.com/articles/s41588-025-02346-4
+      author: [Walfred Ma]({% link Walfred_ma.md %})
+    
 seg_lra:
   - image_path: /software/lra.png
     title: "LRA"
     excerpt: |
       Software for mapping long reads (PacBio/Oxford Nanopore) or their assemblies to genomes. LRA implements an exact convex gap penalty for biologically meaningful gaps to discover structural variation.  
-      git https://github.com/chaissonlab/lra
-
+      git: https://github.com/chaissonlab/lra  
+      bioconda: lra  
+      publication: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009078
+      author: Jingwen Ren
+    
+ seg_danbing-tk:
+   - image_path: /software/danging-tk.png
+     title: danbing-tk
+     excerpt: |
+        A method to map short-read sequences into locus-specific pangenome graphs implemented as de Bruijn graphs to estimate tandem repeat variation by length and composition.  
+     git: https://github.com/chaissonlab/danbing-tk
+     publications: https://genome.cshlp.org/content/33/4/511.short, https://www.nature.com/articles/s41467-021-24378-0
+     author: [Tony Tsung-Yu Lu]({% link tsungyu_lu.md %})
+     
 ---
 {% include feature_row id="seg_ctyper" type="left" %}
 {% include feature_row id="seg_vamos" type="left" %}
 {% include feature_row id="seg_lra" type="left" %}
+{% include feature_row id="seg_danbing-tk" type="left" %}