Engy Nasr

Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

5 Tutorials

• Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition ✍️ 🧐
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data 📝
• Microbiome / Analyses of metagenomics data - The global picture 🧐
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) ✍️

1 Slide

• Sequence analysis / Mapping ✍️

9 FAQs

• After sequencing with MinKNOW software, we get many fastq files, do these files need to be combined into one file before uploading or is it possible to upload them all at once?
• What does `^.*Gallus|Homo|Bos.*$` mean?
• For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?
• From where can I import other genomes?
• Is there a way to filter on the Kalimari database?
• Isn't it awkward to find so many humans sequences there, since we filter for them before?
• Can we use snippy pipeline instead for the phylogenetic analysis?
• Can we also use this workflow on Illumina raw reads?
• Do the pipelines work with both isolates and direct from raw meat? or only isolate?

7 Video Recordings

• Contributing to the Galaxy Training Material / Creating a new tutorial 💬
• Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition 💬 🗣
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data 💬
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) 💬

7 Events

• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Galaxy Training Academy 2025 🧑‍🏫
• From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy 🧑‍🏫
• A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy 🧑‍🏫
• Galaxy Training Academy 2026 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

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GitHub Activity

github Issues Reported

43 Merged Pull Requests

See all of the github Pull Requests and github Commits by Engy Nasr.

• updating Foodborne Muttenz Event Oct 2025, to include Abduallah Kahraman as an organiser
  template-and-tools
• GTN-Foodborne tutorial, updating 2/5 workflows, which contains filter failed datasets tool with the new tool
  microbiome
• adding barchart tool ID to the Allowed_Short_IDs
  template-and-tools
• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
  microbiome
• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
  microbiome

Reviewed 9 PRs

We love our community reviewing each other's work!

• Foodborne workshop event page
  template-and-tools
• Update tutorial.md To include EDAM topics microbiome General Tutorial
  microbiome
• Foodborne Training Updates new PR to the updates since the #4241 PR is blocking my pushes
  metagenomics
• pathogen detection from (direct Nanopore) sequencing data using Galaxy - Updating the training with FAQ and adding an explanation concept
  metagenomics
• Merged foodborne training updates
  metagenomics
  faqs

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