Research engineer in Bioinformatics IRD at Montpellier France
- 🚀 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
- Git
- Conda
- Containers
- Unix basics
- Unix data/file manipulation
- Unix scripting
- Reproducible Research
- Bacterial Comparative Genomics
- Python
- Genome Annotation
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.
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
- 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
- 💪 Opened PR #2 in AnaisDenis/PMosquito
- ❗️ Opened issue #1 in AnaisDenis/PMosquito
- ❌ Unlabeled PR #61812 in bioconda/bioconda-recipes
- 🗣 Commented on #61812 in bioconda/bioconda-recipes
- ❌ Closed PR #579 in NBISweden/AGAT