Merge pull request #4761 from bebatut/mrsa-nanopore-update

Update MRSA Nanopore Assembly tutorial

faqs/galaxy/features_scratchbook.md

@@ -1,20 +1,20 @@
 ---
-title: Using the Scratchbook to view multiple datasets
+title: Using the Window Manager to view multiple datasets
 area: features
 box_type: tip
 layout: faq
 contributors: [shiltemann,hexylena]
 ---
 
-If you would like to view two or more datasets at once, you can use the **Scratchbook** feature in Galaxy:
-  1. **Click** on the *Scratchbook* icon {% icon galaxy-scratchbook%} on the top menu bar.
+If you would like to view two or more datasets at once, you can use the **Window Manager** feature in Galaxy:
+  1. **Click** on the *Window Manager* icon {% icon galaxy-scratchbook%} on the top menu bar.
      - You should see a little checkmark on the icon now
   2. **View** {% icon galaxy-eye %} a dataset by clicking on the eye icon {% icon galaxy-eye %} to view the output
      - You should see the output in a window overlayed over Galaxy
      - You can resize this window by dragging the bottom-right corner
-  3. **Click** outside the file to exit the Scratchbook
+  3. **Click** outside the file to exit the Window Manager
   4. **View** {% icon galaxy-eye %} a second dataset from your history
      - You should now see a second window with the new dataset
      - This makes it easier to compare the two outputs
   5. Repeat this for as many files as you would like to compare
-  6. You can turn off the **Scratchbook** {% icon galaxy-scratchbook %} by clicking on the icon again
+  6. You can turn off the **Window Manager** {% icon galaxy-scratchbook %} by clicking on the icon again

learning-pathways/amr-gene-detection.md

@@ -32,10 +32,8 @@ pathway:
     tutorials:
       - name: mrsa-illumina
         topic: assembly
-#      - name: mrsa-nanopore
-#        topic: assembly
-#      - name: hybrid-assembly
-#        topic: assembly
+      - name: mrsa-nanopore
+        topic: assembly
 
   - section: "Module: Genome annotation"
     description: |

topics/assembly/tutorials/mrsa-nanopore/tutorial.bib

@@ -1,15 +1,26 @@
-@article{Hikichi_2019,
-	doi = {10.1128/mra.01212-19},
-	url = {https://doi.org/10.1128%2Fmra.01212-19},
+@article{Alcock_2019,
+	doi = {10.1093/nar/gkz935},
+	url = {https://doi.org/10.1093%2Fnar%2Fgkz935},
 	year = 2019,
-	month = {nov},
-	publisher = {American Society for Microbiology},
-	volume = {8},
-	number = {47},
-	author = {Miyako Hikichi and Miki Nagao and Kazunori Murase and Chihiro Aikawa and Takashi Nozawa and Akemi Yoshida and Taisei Kikuchi and Ichiro Nakagawa},
-	editor = {Irene L. G. Newton},
-	title = {Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan},
-	journal = {Microbiology Resource Announcements}
+	month = {oct},
+	publisher = {Oxford University Press ({OUP})},
+	author = {Brian P Alcock and Amogelang R Raphenya and Tammy T Y Lau and Kara K Tsang and M{\'{e}}gane Bouchard and Arman Edalatmand and William Huynh and Anna-Lisa V Nguyen and Annie A Cheng and Sihan Liu and Sally Y Min and Anatoly Miroshnichenko and Hiu-Ki Tran and Rafik E Werfalli and Jalees A Nasir and Martins Oloni and David J Speicher and Alexandra Florescu and Bhavya Singh and Mateusz Faltyn and Anastasia Hernandez-Koutoucheva and Arjun N Sharma and Emily Bordeleau and Andrew C Pawlowski and Haley L Zubyk and Damion Dooley and Emma Griffiths and Finlay Maguire and Geoff L Winsor and Robert G Beiko and Fiona S L Brinkman and William W L Hsiao and Gary V Domselaar and Andrew G McArthur},
+	title = {{CARD} 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database},
+	journal = {Nucleic Acids Research}
+}
+
+@article{Carattoli2014,
+  doi = {10.1128/aac.02412-14},
+  url = {https://doi.org/10.1128/aac.02412-14},
+  year = {2014},
+  month = apr,
+  publisher = {American Society for Microbiology},
+  volume = {58},
+  number = {7},
+  pages = {3895--3903},
+  author = {Alessandra Carattoli and Ea Zankari and Aurora Garc{\'{\i}}a-Fern{\'{a}}ndez and Mette Voldby Larsen and Ole Lund and Laura Villa and Frank M{\o}ller Aarestrup and Henrik Hasman},
+  title = {In {SilicoDetection} and Typing of Plasmids using {PlasmidFinder} and Plasmid Multilocus Sequence Typing},
+  journal = {Antimicrobial Agents and Chemotherapy}
 }
 
 @article{Gurevich2013,
@@ -26,6 +37,157 @@ @article{Gurevich2013
   journal = {Bioinformatics}
 }
 
+@article{Hikichi_2019,
+	doi = {10.1128/mra.01212-19},
+	url = {https://doi.org/10.1128%2Fmra.01212-19},
+	year = 2019,
+	month = {nov},
+	publisher = {American Society for Microbiology},
+	volume = {8},
+	number = {47},
+	author = {Miyako Hikichi and Miki Nagao and Kazunori Murase and Chihiro Aikawa and Takashi Nozawa and Akemi Yoshida and Taisei Kikuchi and Ichiro Nakagawa},
+	editor = {Irene L. G. Newton},
+	title = {Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan},
+	journal = {Microbiology Resource Announcements}
+}
+
+@article{koren2017canu,
+  title={Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation},
+  author={Koren, Sergey and Walenz, Brian P and Berlin, Konstantin and Miller, Jason R and Bergman, Nicholas H and Phillippy, Adam M},
+  journal={Genome research},
+  volume={27},
+  number={5},
+  pages={722--736},
+  year={2017},
+  publisher={Cold Spring Harbor Lab},
+	doi={10.1101/gr.215087.116}
+}
+
+@article{Li_2016,
+	author = {Li, Heng},
+	journal = {Bioinformatics},
+	number = {14},
+	year = {2016},
+	month = {3},
+	pages = {2103--2110},
+	publisher = {Oxford University Press (OUP)},
+	title = {Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
+	volume = {32},
+	doi={10.1093/bioinformatics/btw152}
+}
+
+@article{Li_2009,
+	author = {Li, H. and Durbin, R.},
+	journal = {Bioinformatics},
+	number = {14},
+	year = {2009},
+	month = {5},
+	pages = {1754--1760},
+	publisher = {Oxford University Press (OUP)},
+	title = {Fast and accurate short read alignment with {Burrows}-{Wheeler} transform},
+	volume = {25},
+	doi={10.1093/bioinformatics/btp324}
+}
+
+@article{Li_2010,
+	author = {Li, Heng and Durbin, Richard},
+	journal = {Bioinformatics},
+	number = {5},
+	year = {2010},
+	month = {1},
+	pages = {589--595},
+	publisher = {Oxford University Press (OUP)},
+	title = {Fast and accurate long-read alignment with {Burrows}--{Wheeler} transform},
+	volume = {26},
+	doi={10.1093/bioinformatics/btp698}
+}
+
+@misc{Li2013Aligning,
+	author = {Li, Heng},
+	year = {2013},
+	title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA}-{MEM}},
+	howpublished = {http://arxiv.org/abs/1303.3997},
+	doi={10.48550/arXiv.1303.3997}
+}
+
+@article{lin2016assembly,
+  title={Assembly of long error-prone reads using de Bruijn graphs},
+  author={Lin, Yu and Yuan, Jeffrey and Kolmogorov, Mikhail and Shen, Max W and Chaisson, Mark and Pevzner, Pavel A},
+  journal={Proceedings of the National Academy of Sciences},
+  volume={113},
+  number={52},
+  pages={E8396--E8405},
+  year={2016},
+  publisher={National Acad Sciences},
+	doi={10.1073/pnas.1604560113}
+}
+
+
+@article{Lozano_2012,
+	doi = {10.1128/aem.00870-12},
+	url = {https://doi.org/10.1128%2Faem.00870-12},
+	year = 2012,
+	month = {jun},
+	publisher = {American Society for Microbiology},
+	volume = {78},
+	number = {16},
+	pages = {5948--5955},
+	author = {Carmen Lozano and Lourdes Garc{\'{\i}}a-Migura and Carmen Aspiroz and Myriam Zarazaga and Carmen Torres and Frank M{\o}ller Aarestrup},
+	title = {Expansion of a Plasmid Classification System for Gram-Positive Bacteria and Determination of the Diversity of Plasmids in Staphylococcus aureus Strains of Human, Animal, and Food Origins},
+	journal = {Applied and Environmental Microbiology}
+}
+
+@article{vaser2021time,
+  title={Time-and memory-efficient genome assembly with Raven},
+  author={Vaser, Robert and {\v{S}}iki{\'c}, Mile},
+  journal={Nature Computational Science},
+  volume={1},
+  number={5},
+  pages={332--336},
+  year={2021},
+  publisher={Nature Publishing Group US New York},
+	doi={10.1038/s43588-021-00073-4}
+}
+
+@article{Vaser_2017,
+	author = {Vaser, Robert and Sovi{\' c}, Ivan and Nagarajan, Niranjan and {\v S}iki{\' c}, Mile},
+	journal = {Genome Research},
+	number = {5},
+	year = {2017},
+	month = {1},
+	pages = {737--746},
+	publisher = {Cold Spring Harbor Laboratory},
+	title = {Fast and accurate de novo genome assembly from long uncorrected reads},
+	volume = {27},
+	doi={10.1101/gr.214270.116}
+}
+
+@article{wick2015bandage,
+  title={Bandage: interactive visualization of de novo genome assemblies},
+  author={Wick, Ryan R and Schultz, Mark B and Zobel, Justin and Holt, Kathryn E},
+  journal={Bioinformatics},
+  volume={31},
+  number={20},
+  pages={3350--3352},
+  year={2015},
+  publisher={Oxford University Press},
+	doi={10.1093/bioinformatics/btv383}
+}
+
+@article{Wick_2022,
+	author = {Wick, Ryan R. and Holt, Kathryn E.},
+	journal = {PLOS Computational Biology},
+	editor = {Schneidman-Duhovny, Dina},
+	number = {1},
+	year = {2022},
+	month = {1},
+	pages = {e1009802},
+	publisher = {Public Library of Science (PLoS)},
+	title = {Polypolish: Short-read polishing of long-read bacterial genome assemblies},
+	volume = {18},
+	doi={10.1371/journal.pcbi.1009802}
+}
+
 @article{Zankari2012,
   doi = {10.1093/jac/dks261},
   url = {https://doi.org/10.1093/jac/dks261},
@@ -54,43 +216,9 @@ @article{Zankari2017
   journal = {Journal of Antimicrobial Chemotherapy}
 }
 
-@article{Carattoli2014,
-  doi = {10.1128/aac.02412-14},
-  url = {https://doi.org/10.1128/aac.02412-14},
-  year = {2014},
-  month = apr,
-  publisher = {American Society for Microbiology},
-  volume = {58},
-  number = {7},
-  pages = {3895--3903},
-  author = {Alessandra Carattoli and Ea Zankari and Aurora Garc{\'{\i}}a-Fern{\'{a}}ndez and Mette Voldby Larsen and Ole Lund and Laura Villa and Frank M{\o}ller Aarestrup and Henrik Hasman},
-  title = {In {SilicoDetection} and Typing of Plasmids using {PlasmidFinder} and Plasmid Multilocus Sequence Typing},
-  journal = {Antimicrobial Agents and Chemotherapy}
-}
 
 
-@article{Lozano_2012,
-	doi = {10.1128/aem.00870-12},
-	url = {https://doi.org/10.1128%2Faem.00870-12},
-	year = 2012,
-	month = {jun},
-	publisher = {American Society for Microbiology},
-	volume = {78},
-	number = {16},
-	pages = {5948--5955},
-	author = {Carmen Lozano and Lourdes Garc{\'{\i}}a-Migura and Carmen Aspiroz and Myriam Zarazaga and Carmen Torres and Frank M{\o}ller Aarestrup},
-	title = {Expansion of a Plasmid Classification System for Gram-Positive Bacteria and Determination of the Diversity of Plasmids in Staphylococcus aureus Strains of Human, Animal, and Food Origins},
-	journal = {Applied and Environmental Microbiology}
-}
 
 
-@article{Alcock_2019,
-	doi = {10.1093/nar/gkz935},
-	url = {https://doi.org/10.1093%2Fnar%2Fgkz935},
-	year = 2019,
-	month = {oct},
-	publisher = {Oxford University Press ({OUP})},
-	author = {Brian P Alcock and Amogelang R Raphenya and Tammy T Y Lau and Kara K Tsang and M{\'{e}}gane Bouchard and Arman Edalatmand and William Huynh and Anna-Lisa V Nguyen and Annie A Cheng and Sihan Liu and Sally Y Min and Anatoly Miroshnichenko and Hiu-Ki Tran and Rafik E Werfalli and Jalees A Nasir and Martins Oloni and David J Speicher and Alexandra Florescu and Bhavya Singh and Mateusz Faltyn and Anastasia Hernandez-Koutoucheva and Arjun N Sharma and Emily Bordeleau and Andrew C Pawlowski and Haley L Zubyk and Damion Dooley and Emma Griffiths and Finlay Maguire and Geoff L Winsor and Robert G Beiko and Fiona S L Brinkman and William W L Hsiao and Gary V Domselaar and Andrew G McArthur},
-	title = {{CARD} 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database},
-	journal = {Nucleic Acids Research}
-}
+
+