Research engineer in Bioinformatics IRD at Montpellier France

🇦🇹 🇫🇷 🇸🇪

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Personal

• 🚀 I love developing workflows and coding
• 🗨️ Ask me anything about:
  • Bioinformatics
  • Annotation, Assembly, Epitranscriptomics
  • Reproducibility
  • Nextflow (and pipeline in general)
  • GFF/GTF file formats
  • tools that I developed or in which I participated
• 🚂 I'm a curious person and I like to help.
• ✨ I like 🪴 🏞️ and DIY

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Tools (I developed or participated)

Teaching

• Git
• Conda
• Containers
• Unix basics
• Unix data/file manipulation
• Unix scripting
• Reproducible Research
• Bacterial Comparative Genomics
• Python
• Genome Annotation

Conda recipes

I have been involved in the following recipes: RepeatModeler, RepeatMasker, Guessmylt, AGAT, EDTA, Recon, LTR_retriever, Ninja, blast+ (rpsbproc), fingerprintscan, cath-tools, sfld, InterProScan, gaas, gepard, TEsorter, RapGreen, ninja-nj, Craq, IPK, etc.

Cheat sheets and reviews

See here

• Bash cheat sheet A cheat sheet about bash
• Git cheat sheet A cheat sheet about Git
• Screen Cheat Sheet A cheat sheet about Screen
• Coordinate_systems A cheat sheet about coordinate systems in bioinformatics
• Library types Overview of the different library types in RNAseq
• GTF/GFF review Extensive review of the GTF/GFF formats
• Topological sorting of gff features A review of GFF/GTF features sorting in different tools
• GFF to BED conversion A review of different tools to perform GFF to BED conversion
• GFF to GTF conversion A review of different tools to perform GFF to GTF conversion
• Split a FASTA file A review of different tools to split fasta
• The CIGAR string A review the CIGAR string format
• Phasing genome assembly with Falcon Overview on phasing genome assembly with Falcon

Awesomeness

Tutorials

• Gene selection for abinitio tool training A tutorial on gene set filter/selection for training ab initio annotation tools
• Training GeneMark-EP A tutorial on raining GeneMark-EP+ ab-initio tool
• De novo repeat library creation A tutorial about creating de novo repeat library
• Fix-anaconda-licensing-issues A Practical Guide to avoid the pitfalls of the anaconda license
• Shinylive_Quarto A guide to setup R Shiny applications as static web apps using Quarto and Shinylive

Others

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🧰 Languages, Technologies, and Tools

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⚡ Recent Activity

1. ❌ Labeled PR #61527 in bioconda/bioconda-recipes
2. 💪 Opened PR #61527 in bioconda/bioconda-recipes
3. 💪 Opened PR #577 in NBISweden/AGAT
4. ❗️ Closed issue #574 in NBISweden/AGAT
5. ❌ Labeled PR #61484 in bioconda/bioconda-recipes

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