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
Comparative genomics and synteny analysis tool.
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Another Gff Analysis Toolkit.
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Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow.
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Extensive de-novo TE Annotator.
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An efficient way to convert gff3 annotation files into EMBL format ready to submit.
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Genome Assembly and Annotation Service code.
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An efficient way to guess the library type of your RNA-Seq data.
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ctDNA Analysis pipeline.
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A set of workflows written in Nextflow for Genome Annotation.
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RNA Alterations Investigation using Nextflow with particular focus on A-to-I editing events.
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Small utility to visualise read alignment directly from sam format without reference.
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Summarize Alignment Pile by Nucleotide.
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TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes.
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- 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.
- 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
A list of awesome awesomeness related to bioinformatics and associated fields.
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Awesome genome/mitome/plastome/plastidome annotation tool list.
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A list of awesome bioinformatics communities.
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A curated list of awesome blog in bioinformatics and affiliated areas.
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- 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
A Bioinformatics Nextflow Pipeline Template.
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My collection of cheat sheets / overviews / summaries and more.
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CI workflow to automatically publish selected RSS feeds to a Bluesky account (use case: https://bsky.app/profile/bioinfoblogs.bsky.social).
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- ❌ Merged PR #49 in Juke34/AliNe
- 💪 Opened PR #49 in Juke34/AliNe
- ❌ Closed PR #55 in Juke34/RAIN
- ❌ Merged PR #11 in MargauxLefebvre/ViroSeek
- 🗣 Commented on #11 in MargauxLefebvre/ViroSeek
