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.
See here
* [Bash cheat sheet](https://juke34.github.io/knowledge/programming/bash/bash_cheat_sheet/) A cheat sheet about bash * [Git cheat sheet](https://juke34.github.io/knowledge/programming/git/git/#tagging) A cheat sheet about Git * [Screen Cheat Sheet](https://juke34.github.io/knowledge/cluster/screen/) A cheat sheet about Screen * [Coordinate_systems](https://github.com/Juke34/coordinate_systems) A cheat sheet about coordinate systems in bioinformaticsSee here
* [Library types](https://joss.theoj.org/papers/10.21105/joss.01344) Overview of the different library types in RNAseq * [GTF/GFF review](https://nbisweden.github.io/AGAT/gxf/) Extensive review of the GTF/GFF formats * [Topological sorting of gff features](https://nbisweden.github.io/AGAT/topological-sorting-of-gff-features/) A review of GFF/GTF features sorting in different tools * [GFF to BED conversion](https://nbisweden.github.io/AGAT/gff_to_bed/) A review of different tools to perform GFF to BED conversion * [GFF to GTF conversion](https://nbisweden.github.io/AGAT/gff_to_gtf/) A review of different tools to perform GFF to GTF conversion * [Split a FASTA file](https://juke34.github.io/knowledge/bioinformatics/format/handling/split_fasta/) A review of different tools to split fasta * [The CIGAR string](https://juke34.github.io/knowledge/bioinformatics/format/specification/cigar/) A review the CIGAR string format * [Phasing genome assembly with Falcon](https://www.biostars.org/p/426259/) Overview on phasing genome assembly with FalconSee here
* [Awesome awesomeness bioinformatics](https://github.com/Juke34/awesome-awesomeness-bioinformatics) A list of awesome awesomeness related to bioinformatics and associated fields * [Awesome genome annotation](https://juke34.github.io/awesome-genome-annotation/) Awesome genome/mitome/plastome/plastidome annotation tool list * [Awesome bioinformatics community](https://github.com/Juke34/awesome-community-bioinformatics) A list of awesome bioinformatics communities * [Awesome bioinformatics blog](https://github.com/Juke34/awesome-blog-bioinformatics) A list of awesome bioinformatics blogsSee here
* [Gene selection for abinitio tool training ](https://www.biostars.org/p/394385/#9542649) A tutorial on gene set filter/selection for training ab initio annotation tools * [Training GeneMark-EP](https://www.biostars.org/p/420356/) A tutorial on raining GeneMark-EP+ ab-initio tool * [De novo repeat library creation](https://www.biostars.org/p/411101/) A tutorial about creating de novo repeat library * [fix-anaconda-licensing-issues](https://juke34.github.io/fix-anaconda-licensing-issues/en/) A Practical Guide to avoid the pitfalls of the anaconda licenseSee here
* [BiTeN](https://github.com/Juke34/BiTeN) A Bioinformatics Nextflow Pipeline Template * [Knowledge](https://juke34.github.io/knowledge/) My collection of cheat sheets / overviews / summaries and more
GitHub
- 🗣 Commented on #517 in NBISweden/AGAT
- 🗣 Commented on #516 in NBISweden/AGAT
- 🗣 Commented on #513 in NBISweden/AGAT
- 🗣 Commented on #512 in NBISweden/AGAT
- 💪 Opened PR #515 in NBISweden/AGAT