Hi there 👋, I'm Jacques

Research engineer in Bioinformatics IRD at Montpellier France

🇦🇹 🇫🇷 🇸🇪

Personal

🚀 I love developing workflows and coding
🗨️ Ask me anything about:
- Bioinformatics
- Annotation, Assembly, Epitranscriptomics
- 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

Tools (I developed or participated)

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 (bowtie2, bwa aln, bwa mem, bwa sw, graphmap2, hisat2, minimap2, nucmer, star, star 2pass mode).
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

Teaching

Conda

Recipes: RepeatModeler, RepeatMasker, Guessmylt, AGAT, EDTA, Recon, LTR_retriever, Ninja, blast+ (rpsbproc), fingerprintscan, sfld, InterProScan, gaas, gepard, TEsorter, RapGreen, ninja-nj, Craq, etc.

Others

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 community bioinformatics A list of awesome bioinformatics communities
Coordinate_systems A cheat sheet about coordinate systems in bioinformatics
Library types Overview of the different library types in RNAseq
Knowledge My collection of cheat sheets / overviews / summaries
BiTeN A Bioinformatics Nextflow Pipeline Template