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.

Tutorials

• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data
• Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition ✍️

Slides

• Sequence analysis / Mapping ✍️

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?

Video Recordings

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

Events

• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

40 Merged Pull Requests

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

• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
  microbiome
• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
  microbiome
• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition - Training update to latest workflows update
  microbiome
• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, training update 2024
  microbiome
• Adding EDAM topics to genome annotation gene centric tutorial
  genome-annotation

Reviewed 8 PRs

We love our community reviewing each other's work!

• 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
• fixing typos in pathogen detection
  metagenomics

News

External Links

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