Add 'Quality and contamination control in bacterial isolate using Illumina MiSeq Data' tutorial

CONTRIBUTORS.yaml

@@ -498,6 +498,10 @@ claresloggett:
 
 clsiguret:
     name: Clea Siguret
+    email: [email protected]
+    linkedin: cléa-siguret-58423b107
+    matrix: 'clsiguret:matrix.org'
+    orcid: 0009-0005-6140-0379
     joined: 2024-04
     elixir_node: fr
     affiliations:

learning-pathways/amr-gene-detection.md

@@ -8,6 +8,7 @@ tags: [amr, bacteria, microgalaxy, one-health]
 
 editorial_board:
 - bebatut
+- clsiguret
 funding:
 - abromics
 
@@ -21,10 +22,10 @@ pathway:
 
   - section: "Module: Species and contamination checking"
     description: |
-      Taxonomic assignation is useful in AMR detection to check contamination and confirm species
+      Quality control and taxonomic assignation is useful in AMR detection to verify the quality of the data but also to check contamination and confirm species
     tutorials:
-      - name: bacterial-isolate-species-contamination-checking
-        topic: ecology
+      - name: quality-contamination-control
+        topic: sequence-analysis
 
   - section: "Module: Assembly"
     description: |

topics/sequence-analysis/tutorials/quality-contamination-control/data-library.yaml

@@ -0,0 +1,27 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Sequence analysis
+  description: Analyses of sequences
+  items:
+  - name: Quality and contamination control in bacterial isolate using Illumina MiSeq Data
+    items:
+    - name: 'DOI: 10.5281/zenodo.10669812'
+      description: latest
+      items:
+      - url: https://zenodo.org/records/10669812/files/DRR187559_1.fastqsanger.bz
+        src: url
+        ext: fastqsanger.bz2
+        info: https://doi.org/10.5281/zenodo.10669812
+      - url: https://zenodo.org/records/10669812/files/DRR187559_2.fastqsanger.bz
+        src: url
+        ext: fastqsanger.bz2
+        info: https://doi.org/10.5281/zenodo.10669812
+      - url: https://zenodo.org/records/10669812/files/DRR187567.fastq.bz
+        src: url
+        ext: fastq.bz2
+        info: https://doi.org/10.5281/zenodo.10669812

topics/sequence-analysis/tutorials/quality-contamination-control/faqs/index.md

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

topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.bib

@@ -0,0 +1,97 @@
+@article{Bushnell2017,
+  title = {BBMerge - Accurate paired shotgun read merging via overlap},
+	author = {Bushnell, Brian and Rood, Jonathan and Singer, Esther},
+	editor = {Biggs, Patrick Jon},
+	number = {10},
+	year = {2017},
+	month = {10},
+	pages = {e0185056},
+  volume = {12},
+	publisher = {Public Library of Science (PLoS)},
+	doi = {10.1371/journal.pone.0185056},
+  url = {https://doi.org/10.1371/journal.pone.0185056}
+}
+
+@article{Chen2018,
+  author = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
+  year = {2018},
+  month = {3},
+  publisher = {Cold Spring Harbor Laboratory},
+  title = {fastp: an ultra-fast all-in-one {FASTQ} preprocessor},
+  doi={10.1093/bioinformatics/bty560},
+}
+
+@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{Lu.2017,
+  author = {Lu, Jennifer and Breitwieser, Florian P. and Thielen, Peter and Salzberg, Steven L.},
+  year = {2017},
+  title = {Bracken: estimating species abundance in metagenomics data},
+  pages = {e104},
+  volume = {3},
+  journal = {PeerJ Computer Science},
+  doi = {10.7717/peerj-cs.104}
+}
+
+@article{marti2019recentrifuge,
+  title={Recentrifuge: Robust comparative analysis and contamination removal for metagenomics},
+  author={Mart{\'\i}, Jose Manuel},
+  journal={PLoS computational biology},
+  volume={15},
+  number={4},
+  pages={e1006967},
+  year={2019},
+  publisher={Public Library of Science San Francisco, CA USA},
+  doi = {10.1371/journal.pcbi.100696}
+}
+
+@article{Parks_2015,
+	author = {Parks, Donovan H. and Imelfort, Michael and Skennerton, Connor T. and Hugenholtz, Philip and Tyson, Gene W.},
+  doi = {10.1101/gr.186072.114},
+	journal = {Genome Research},
+	number = {7},
+	year = {2015},
+	month = {5},
+	pages = {1043--1055},
+	publisher = {Cold Spring Harbor Laboratory},
+	title = {CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes},
+	volume = {25},
+}
+
+@article{wood2019improved,
+  title={Improved metagenomic analysis with Kraken 2},
+  author={Wood, Derrick E and Lu, Jennifer and Langmead, Ben},
+  journal={Genome biology},
+  volume={20},
+  number={1},
+  pages={1--13},
+  year={2019},
+  publisher={Springer},
+  doi={10.1186/s13059-019-1891-0}
+}
+
+
+@article{Ye.2019,
+  abstract = {Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.},
+  author = {Ye, Simon H. and Siddle, Katherine J. and Park, Daniel J. and Sabeti, Pardis C.},
+  year = {2019},
+  title = {Benchmarking Metagenomics Tools for Taxonomic Classification},
+  pages = {779--794},
+  volume = {178},
+  number = {4},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2019.07.010},
+  file = {Ye, Siddle et al. 2019 - Benchmarking Metagenomics Tools for Taxonomic:Attachments/Ye, Siddle et al. 2019 - Benchmarking Metagenomics Tools for Taxonomic.pdf:application/pdf}
+}