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
See here
- AGAT Suite of tools to handle gene annotations in any GTF/GFF format.
- AliNe A pipeline to automate alignment using the aligners of your choice (over 12 different aligners available).
- EMBLmyGFF3 A tool to converts an assembly in FASTA format along with associated annotation in GFF3 format into the EMBL flat file format which is the required format for submitting annotated assemblies to ENA. Paper
- GAAS Suite of tools related to Genome Assembly and Annotation tasks.
- GUESSmyLT A tool to guess the library type of your RNA-Seq data. Paper
- pipelines-nextflow A set of workflows written in Nextflow for Genome Annotation.
- SAPiN A tool that aims to summarize SAM/BAM read alignment by pileup or reads at each position in a tabulated way.
- SamReadViewer A small utility to visualise read alignments directly from SAM format without reference.
- TeSorter An accurate and fast method to classify LTR-retrotransposons in plant genomes. Paper
- EDTA The Extensive de novo TE Annotator (EDTA). Paper
- baargin Bacterial Assembly and Antimicrobial Resistance Genes detection In NextFlow. Paper
See here
See here
I have been involved in the following recipes: RepeatModeler, RepeatMasker, Guessmylt, AGAT, EDTA, Recon, LTR_retriever, Ninja, blast+ (rpsbproc), fingerprintscan, sfld, InterProScan, gaas, gepard, TEsorter, RapGreen, ninja-nj, Craq, IPK, etc.
- Awesome awesomeness bioinformatics A list of awesome awesomeness related to bioinformatics and associated fields
- Awesome genome annotation Awesome genome/mitome/plastome/plastidome annotation tool list
- Awesome bioinformatics community A list of awesome bioinformatics communities
- Awesome bioinformatics blog A list of awesome bioinformatics blogs
- BiTeN A Bioinformatics Nextflow Pipeline Template
- Coordinate_systems A cheat sheet about coordinate systems in bioinformatics
- fix-anaconda-licensing-issues A Practical Guide to avoid the pitfalls of the anaconda license
- Knowledge My collection of cheat sheets / overviews / summaries
- Library types Overview of the different library types in RNAseq
GitHub
- 🗣 Commented on #13 in colindaven/awesome-pangenomes
- 🗣 Commented on #508 in NBISweden/AGAT
- 💪 Opened PR #13 in colindaven/awesome-pangenomes
- 🗣 Commented on #508 in NBISweden/AGAT
- 🗣 Commented on #7348 in openjournals/joss-reviews