Add new tutorial for deciphering viral populations using SNV and baculovirus isolates (Variant analysis)

CONTRIBUTORS.yaml

@@ -1148,6 +1148,19 @@ jfallmann:
     name: Joerg Fallmann
     joined: 2017-09
 
+wennj:
+    name: Jörg Wennmann
+    email: [email protected]
+    orcid: 0000-0003-3060-8992
+    contact_for_training: true
+    joined: 2025-01
+    location:
+      country: DE
+      lat: 49.449466
+      lon: 8.640339
+    affiliations:
+      - jki
+
 jfaulon:
     name: Jean-Loup Faulon
     email: [email protected]

Gemfile.lock

@@ -1,21 +1,24 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.8.5)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     awesome_bot (1.20.0)
       parallel (= 1.20.1)
-    bibtex-ruby (6.0.0)
+    bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
+      racc (~> 1.7)
+    bigdecimal (3.1.9)
     citeproc (1.0.10)
       namae (~> 1.0)
-    citeproc-ruby (2.0.0)
+    citeproc-ruby (2.1.0)
       citeproc (~> 1.0, >= 1.0.9)
       csl (~> 2.0)
+      observer (< 1.0)
     colorator (1.1.0)
-    commander (4.6.0)
-      highline (~> 2.0.0)
-    concurrent-ruby (1.2.2)
+    commander (5.0.0)
+      highline (~> 3.0.0)
+    concurrent-ruby (1.3.5)
     csl (2.0.0)
       namae (~> 1.0)
       rexml
@@ -28,12 +31,32 @@ GEM
     ethon (0.16.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    fastimage (2.2.7)
-    ffi (1.16.2)
+    fastimage (2.4.0)
+    ffi (1.17.1-aarch64-linux-gnu)
+    ffi (1.17.1-aarch64-linux-musl)
+    ffi (1.17.1-arm-linux-gnu)
+    ffi (1.17.1-arm-linux-musl)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.1-x86_64-linux-musl)
     forwardable-extended (2.6.0)
-    google-protobuf (3.25.5-x86_64-darwin)
-    google-protobuf (3.25.5-x86_64-linux)
-    highline (2.0.3)
+    google-protobuf (4.29.3)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-aarch64-linux)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-x86_64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-x86_64-linux)
+      bigdecimal
+      rake (>= 13)
+    highline (3.0.1)
     html-proofer (4.4.3)
       addressable (~> 2.3)
       mercenary (~> 0.3)
@@ -44,9 +67,9 @@ GEM
       yell (~> 2.0)
       zeitwerk (~> 2.5)
     http_parser.rb (0.8.0)
-    i18n (1.14.1)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
-    jekyll (4.3.2)
+    jekyll (4.3.4)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -70,59 +93,96 @@ GEM
       sass-embedded (~> 1.54)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (2.4.0)
-      rexml
+    kramdown (2.5.1)
+      rexml (>= 3.3.9)
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
     kwalify (0.7.2)
     latex-decode (0.4.0)
     liquid (4.0.4)
-    listen (3.8.0)
+    listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
-    namae (1.1.1)
-    nokogiri (1.16.5-x86_64-darwin)
+    namae (1.2.0)
+      racc (~> 1.7)
+    nokogiri (1.18.1-aarch64-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-aarch64-linux-musl)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm-linux-gnu)
+      racc (~> 1.4)
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+    nokogiri (1.18.1-x86_64-linux-gnu)
       racc (~> 1.4)
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+    nokogiri (1.18.1-x86_64-linux-musl)
       racc (~> 1.4)
+    observer (0.1.2)
     parallel (1.20.1)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    pkg-config (1.5.5)
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+    psych (5.2.3)
       date
       stringio
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-    racc (1.8.0)
+    public_suffix (6.0.1)
+    racc (1.8.1)
     rainbow (3.1.1)
+    rake (13.2.1)
     rb-fsevent (0.11.2)
-    rb-inotify (0.10.1)
+    rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rdoc (6.9.1)
+    rdoc (6.11.0)
       psych (>= 4.0.0)
-    rexml (3.3.9)
+    rexml (3.4.0)
     rorvswild_theme_rdoc (0.2)
-    rouge (4.1.3)
+    rouge (4.5.1)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
-    sass-embedded (1.69.5-x86_64-darwin)
-      google-protobuf (~> 3.23)
-    sass-embedded (1.69.5-x86_64-linux-gnu)
-      google-protobuf (~> 3.23)
+    sass-embedded (1.83.4-aarch64-linux-gnu)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-aarch64-linux-musl)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm-linux-gnueabihf)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm-linux-musleabihf)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm64-darwin)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-darwin)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-linux-gnu)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-linux-musl)
+      google-protobuf (~> 4.29)
     stringio (3.1.2)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
-    typhoeus (1.4.0)
+    typhoeus (1.4.1)
       ethon (>= 0.9.0)
-    unicode-display_width (2.5.0)
-    webrick (1.8.2)
+    unicode-display_width (2.6.0)
+    webrick (1.9.1)
     yell (2.2.2)
-    zeitwerk (2.6.12)
+    zeitwerk (2.7.1)
 
 PLATFORMS
-  x86_64-darwin-19
+  aarch64-linux
+  aarch64-linux-gnu
+  aarch64-linux-musl
+  arm-linux-gnu
+  arm-linux-gnueabihf
+  arm-linux-musl
+  arm-linux-musleabihf
+  arm64-darwin
+  x86_64-darwin
   x86_64-linux
+  x86_64-linux-gnu
+  x86_64-linux-musl
 
 DEPENDENCIES
   addressable
@@ -145,4 +205,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.4.20
+   2.6.2

topics/variant-analysis/tutorials/baculovirus-isolate-variation/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.bib

@@ -0,0 +1,147 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@article{vanOers2007,
+  title = {Baculovirus Genomics},
+  volume = {8},
+  ISSN = {1389-4501},
+  url = {http://dx.doi.org/10.2174/138945007782151333},
+  DOI = {10.2174/138945007782151333},
+  number = {10},
+  journal = {Current Drug Targets},
+  publisher = {Bentham Science Publishers Ltd.},
+  author = {van Oers,  Monique and Vlak,  Just},
+  year = {2007},
+  month = oct,
+  pages = {1051–1068}
+}
+
+@article{Fan2020,
+  title = {Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation},
+  volume = {7},
+  ISSN = {2057-1577},
+  url = {http://dx.doi.org/10.1093/ve/veaa073},
+  DOI = {10.1093/ve/veaa073},
+  number = {1},
+  journal = {Virus Evolution},
+  publisher = {Oxford University Press (OUP)},
+  author = {Fan,  Jiangbin and Jehle,  Johannes A and Wennmann,  J\"{o}rg T},
+  year = {2020},
+  month = sep 
+}
+
+@article{Wennmann2024,
+  title = {Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants},
+  volume = {105},
+  ISSN = {1465-2099},
+  url = {http://dx.doi.org/10.1099/jgv.0.001983},
+  DOI = {10.1099/jgv.0.001983},
+  number = {5},
+  journal = {Journal of General Virology},
+  publisher = {Microbiology Society},
+  author = {Wennmann,  J\"{o}rg T. and Lim,  Fang-Shiang and Senger,  Sergei and Gani,  Mudasir and Jehle,  Johannes A. and Keilwagen,  Jens},
+  year = {2024},
+  month = may 
+}
+
+@misc{ICTV_AcMNPV_genome_figure,
+  author = {International Committee on Taxonomy of Viruses (ICTV)},
+  title = {Genome mag of Autographa californica multiple nucleopolyhedrovirus isolate C6 (Figure 2)},
+  url = {\url{https://ictv.global/sites/default/files/inline-images/7651.ODD.Baculo.Fig2.v2.png}},
+  urldate = {2024-12-27}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}
+
+@article{Harrison2018,
+  title = {ICTV Virus Taxonomy Profile: Baculoviridae},
+  volume = {99},
+  ISSN = {1465-2099},
+  url = {http://dx.doi.org/10.1099/jgv.0.001107},
+  DOI = {10.1099/jgv.0.001107},
+  number = {9},
+  journal = {Journal of General Virology},
+  publisher = {Microbiology Society},
+  author = {Harrison,  Robert L. and Herniou,  Elisabeth A. and Jehle,  Johannes A. and Theilmann,  David A. and Burand,  John P. and Becnel,  James J. and Krell,  Peter J. and van Oers,  Monique M. and Mowery,  Joseph D. and Bauchan,  Gary R.},
+  year = {2018},
+  month = sep,
+  pages = {1185–1186}
+}
+
+@article{Ayres1994,
+  title = {The Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis Virus},
+  volume = {202},
+  ISSN = {0042-6822},
+  url = {http://dx.doi.org/10.1006/viro.1994.1380},
+  DOI = {10.1006/viro.1994.1380},
+  number = {2},
+  journal = {Virology},
+  publisher = {Elsevier BV},
+  author = {Ayres,  Martin D. and Howard,  Stephen C. and Kuzio,  John and Lopez-Ferber,  Miguel and Possee,  Robert D.},
+  year = {1994},
+  month = aug,
+  pages = {586–605}
+}
+
+@misc{sequence-analysis-quality-control,
+author = "Bérénice Batut and Maria Doyle and Alexandre Cormier and Anthony Bretaudeau and Laura Leroi and Erwan Corre and Stéphanie Robin and Cameron Hyde",
+	title = "Quality Control (Galaxy Training Materials)",
+	year = "",
+	month = "",
+	day = "",
+	url = "\url{https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html}",
+	note = "[Online; accessed Wed Jan 08 2025]"
+}
+
+@article{Wennmann2020,
+  title = {Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses},
+  volume = {12},
+  ISSN = {1999-4915},
+  url = {http://dx.doi.org/10.3390/v12060625},
+  DOI = {10.3390/v12060625},
+  number = {6},
+  journal = {Viruses},
+  publisher = {MDPI AG},
+  author = {Wennmann,  J\"{o}rg T. and Fan,  Jiangbin and Jehle,  Johannes A.},
+  year = {2020},
+  month = jun,
+  pages = {625}
+}