{"id":25977661,"url":"https://github.com/juke34/juke34","last_synced_at":"2026-03-09T03:33:25.665Z","repository":{"id":37718233,"uuid":"297303852","full_name":"Juke34/Juke34","owner":"Juke34","description":"repository used to add a README.md to the GitHub 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-05T04:38:49.892Z","updated_at":"2026-03-09T03:33:20.654Z","avatar_url":"https://github.com/Juke34.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\u003cdiv align=center \u003e\n\u003cimg src=\"https://readme-typing-svg.herokuapp.com?font=Pacifico\u0026size=25\u0026color=FFFFFF\u0026center=true\u0026lines=Hey+hey+👋%2C+I'm+Jacques+Dainat.;Senior+Bioinformatician.\"\n/\u003e \u003cimg src=\"https://media.giphy.com/media/6Nk9AFUDuPHgXp31xT/giphy.gif\" width=\"50\"\u003e\n\u003c/div\u003e\n\n\u003ch3 align=\"center\"\u003e \u003cem\u003eResearch engineer in Bioinformatics \u003ca href=\"https://www.ird.fr\"\u003eIRD\u003c/a\u003e at Montpellier France\u003c/em\u003e\u003c/h3\u003e\n\u003ch1 align=\"center\"\u003e 🇦🇹 🇫🇷 🇸🇪 \u003c/h1\u003e\n\n\u003cdiv align=\"center\"\u003e\n  \n  \u003ca href=\"\"\u003e[![GitHub Juke34](https://img.shields.io/github/followers/Juke34?label=follow\u0026style=social)](https://github.com/Juke34)\u003c/a\u003e\n  \u003ca href=\"\"\u003e[![Twitter: jacquesdainat](https://img.shields.io/badge/bluesky-Follow-blue?logo=bluesky)](https://bsky.app/profile/jacquesdainat.bsky.social)\u003c/a\u003e\n  \u003ca href=\"\"\u003e[![Mastodon: jacquesdainat](https://img.shields.io/mastodon/follow/109364780903162240?domain=https%3A%2F%2Fgenomic.social)](https://genomic.social/@jacquesdainat)\u003c/a\u003e  \n  \u003c!-- \u003ca href=\"\"\u003e![](https://komarev.com/ghpvc/?username=Juke34\u0026style=flat-square)\u003c/a\u003e--\u003e\n\u003c/div\u003e\n\n\u003cdiv style=\"float: right\"\u003e\n  \u003ca href=\"https://github.com/Juke34/github-readme-stats\" title=\"GitHub Readme Stats\"\u003e\n      \u003cimg src=\"https://github-readme-stats.juke34.vercel.app/api?username=Juke34\u0026count_private=true\u0026show_icons=true\u0026hide_border=true\u0026theme=tokyonight\u0026hide=stars\" width=45%\" height=\"220\" align=\"right\" alt=\"github stats\" /\u003e\n  \u003c/a\u003e\n\u003c/div\u003e\n\n\u003cdiv align=\"center\"\u003e\n  \n### Now Playing — Spotify 🎧\n      \n  [![spotify-github-profile](https://spotify-github-profile.kittinanx.com/api/view?uid=keujmat\u0026cover_image=true\u0026theme=novatorem\u0026show_offline=false\u0026background_color=121212\u0026interchange=false\u0026bar_color=53b14f\u0026bar_color_cover=false)](https://spotify-github-profile.kittinanx.com/api/view?uid=keujmat\u0026redirect=true)\n    \n\n\u003c/div\u003e\n\n### :octocat: Personal\n  \n- 🚀 I love developing workflows and coding\n- 🗨️ Ask me anything about:\n    - Bioinformatics\n    - Annotation, Assembly, Epitranscriptomics\n    - Reproducibility\n    - Nextflow (and pipeline in general)\n    - GFF/GTF file formats\n    - tools that I developed or in which I participated\n- 🚂 I'm a curious person and I like to help. \n- ✨ I like 🪴 🏞️ and DIY\n\n---\n\n### Tools (I developed or participated)\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n\n* [AGAT](https://github.com/NBISweden/AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.\n* [AliNe](https://github.com/Juke34/AliNe) A pipeline to automate alignment using the aligners of your choice (over 12 different aligners available).\n* [EMBLmyGFF3](https://github.com/NBISweden/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](https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-018-3686-x)\n* [GAAS](https://github.com/NBISweden/GAAS) Suite of tools related to Genome Assembly and Annotation tasks.\n* [GUESSmyLT](https://github.com/NBISweden/GUESSmyLT) A tool to guess the library type of your RNA-Seq data. [Paper](https://joss.theoj.org/papers/10.21105/joss.01344)\n* [pipelines-nextflow](https://github.com/NBISweden/pipelines-nextflow) A set of workflows written in Nextflow for Genome Annotation.\n* [SAPiN](https://github.com/Juke34/SAPiN) A tool that aims to summarize SAM/BAM read alignment by pileup or reads at each position in a tabulated way. \n* [SamReadViewer](https://juke34.github.io/SamReadViewer/sam2view.html) A small utility to visualise read alignments directly from SAM format without reference.\n* [TeSorter](https://github.com/zhangrengang/TEsorter) An accurate and fast method to classify LTR-retrotransposons in plant genomes. [Paper](https://academic.oup.com/hr/article/doi/10.1093/hr/uhac017/6532211?login=true)\n* [EDTA](https://github.com/oushujun/EDTA) The Extensive de novo TE Annotator (EDTA). [Paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y)\n* [baargin](https://github.com/jhayer/baargin) Bacterial Assembly and Antimicrobial Resistance Genes detection In NextFlow. [Paper](https://joss.theoj.org/papers/10.21105/joss.05397)\n\n\u003c/details\u003e\n\n### Teaching\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [Git](https://mivegec.pages.ird.fr/dainat/malbec-git/)\n* [Conda](https://mivegec.pages.ird.fr/dainat/malbec-conda/)\n* [Containers](https://mivegec.pages.ird.fr/dainat/malbec-containers/)\n* [Unix basics](https://mivegec.pages.ird.fr/dainat/malbec-unix)\n* [Unix data/file manipulation](https://mivegec.pages.ird.fr/dainat/malbec-unix)\n* [Unix scripting](https://mivegec.pages.ird.fr/dainat/malbec-unix)\n* [Reproducible Research](https://southgreenplatform.github.io/training_reproducible_research/)\n* [Bacterial Comparative Genomics](https://southgreenplatform.github.io/training_bacterial_comparative_genomics/)\n* [Python](https://southgreenplatform.github.io/training_python/)\n* [Annotation](https://nbisweden.github.io/workshop-genome_annotation_elixir/)\n\n\u003c/details\u003e\n\n### Conda recipes\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n  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.\n\n\u003c/details\u003e\n\n### Cheat sheets\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [Bash cheat sheet](https://juke34.github.io/knowledge/programming/bash/bash_cheat_sheet/) A cheat sheet about bash\n* [Git cheat sheet](https://juke34.github.io/knowledge/programming/git/git/#tagging) A cheat sheet about Git\n* [Screen Cheat Sheet](https://juke34.github.io/knowledge/cluster/screen/) A cheat sheet about Screen\n* [Coordinate_systems](https://github.com/Juke34/coordinate_systems) A cheat sheet about coordinate systems in bioinformatics\n\u003c/details\u003e\n\n### Reviews\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [Library types](https://joss.theoj.org/papers/10.21105/joss.01344) Overview of the different library types in RNAseq\n* [GTF/GFF review](https://nbisweden.github.io/AGAT/gxf/) Extensive review of the GTF/GFF formats\n* [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\n* [GFF to BED conversion](https://nbisweden.github.io/AGAT/gff_to_bed/) A review of different tools to perform GFF to BED conversion\n* [GFF to GTF conversion](https://nbisweden.github.io/AGAT/gff_to_gtf/) A review of different tools to perform GFF to GTF conversion\n* [Split a FASTA file](https://juke34.github.io/knowledge/bioinformatics/format/handling/split_fasta/) A review of different tools to split fasta\n* [The CIGAR string](https://juke34.github.io/knowledge/bioinformatics/format/specification/cigar/) A review the CIGAR string format\n* [Phasing genome assembly with Falcon](https://www.biostars.org/p/426259/) Overview on phasing genome assembly with Falcon\n\u003c/details\u003e\n\n### Awesomeness\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [Awesome awesomeness bioinformatics](https://github.com/Juke34/awesome-awesomeness-bioinformatics) A list of awesome awesomeness related to bioinformatics and associated fields\n* [Awesome genome annotation](https://juke34.github.io/awesome-genome-annotation/) Awesome genome/mitome/plastome/plastidome annotation tool list\n* [Awesome bioinformatics community](https://github.com/Juke34/awesome-community-bioinformatics) A list of awesome bioinformatics communities\n* [Awesome bioinformatics blog](https://github.com/Juke34/awesome-blog-bioinformatics) A list of awesome bioinformatics blogs\n\u003c/details\u003e\n\n### Tutorials\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [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\n* [Training GeneMark-EP](https://www.biostars.org/p/420356/) A tutorial on raining GeneMark-EP+ ab-initio tool\n* [De novo repeat library creation](https://www.biostars.org/p/411101/) A tutorial about creating de novo repeat library \n* [fix-anaconda-licensing-issues](https://juke34.github.io/fix-anaconda-licensing-issues/en/) A Practical Guide to avoid the pitfalls of the anaconda license\n\u003c/details\u003e\n\n### Others\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee here\u003c/summary\u003e\n  \n* [BiTeN](https://github.com/Juke34/BiTeN) A Bioinformatics Nextflow Pipeline Template\n* [Knowledge](https://juke34.github.io/knowledge/) My collection of cheat sheets / overviews / summaries and more\n\u003c/details\u003e\n\n---\n\n### 🧰 Languages, Technologies, and Tools\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/topics/python\" title=\"Python\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/python/python.png\" alt=\"python logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/perl\" title=\"Perl\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/perl/perl.png\" alt=\"perl logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/bash\" title=\"Bash\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/bash/bash.png\" alt=\"bash logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/r\" title=\"R\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/r/r.png\" alt=\"R logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/java\" title=\"Java\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/java/java.png\" alt=\"java logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/git\" title=\"Git\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/git/git.png\" alt=\"git logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/macos\" title=\"macos\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/macos/macos.png\" alt=\"linux macos\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/linux\" title=\"Linux\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/linux/linux.png\" alt=\"linux logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/terminal\" title=\"Terminal\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/d92924b1d925bb134e308bd29c9de6c302ed3beb/topics/terminal/terminal.png\" alt=\"terminal logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/Visual_Studio_Code\" title=\"VSCode\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/bbd48b997e8d0bef63f676eca4da5e1f76487b56/topics/visual-studio-code/visual-studio-code.png\" alt=\"VSCode logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/Nextflow\" title=\"Nextflow\"\u003e\u003cimg src=\"https://github.com/nextflow-io/nextflow/raw/master/docs/_static/nextflow-logo-bg-dark.png\" alt=\"nextflow logo\" width=\"120\" height=\"28\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/snakemake\" title=\"Snakemake\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/snakemake/snakemake/6fcdc8a22db5522e232638bff16da9b50996eb45/images/logo.svg\" alt=\"snakemake logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/bioconda\" title=\"Bioconda\"\u003e\u003cimg src=\"http://bioconda.github.io/_images/bioconda.png\" alt=\"bioconda logo\" width=\"120\" height=\"22\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/slack\" title=\"slack\"\u003e\u003cimg src=\"https://cdn.worldvectorlogo.com/logos/slack-new-logo.svg\" alt=\"slack logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/discord\" title=\"discord\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/2a3ce46f963399611d8e2054bb0ce9a4b539296a/topics/discord/discord.png\" alt=\"discord logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/topics/docker\" title=\"docker\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/github/explore/80688e429a7d4ef2fca1e82350fe8e3517d3494d/topics/docker/docker.png\" alt=\"docker logo\" width=\"36\" height=\"36\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/topics/singularity\" title=\"singularity\"\u003e\u003cimg src=\"https://insidehpc.com/wp-content/uploads/2017/05/singularity.jpg\" alt=\"singularity logo\" width=\"40\" height=\"36\" /\u003e\u003c/a\u003e\n  \n\u003c/p\u003e\n\n---\n\n### ⚡ Recent Activity\n\n\u003cdetails\u003e\n  \u003csummary\u003eGitHub\u003c/summary\u003e\n\n\u003c!--START_SECTION:activity--\u003e\n1. 🗣 Commented on [#7545](https://github.com//openjournals/joss-reviews/issues/7545) in [openjournals/joss-reviews](https://github.com//openjournals/joss-reviews)\n2. 🗣 Commented on [#7545](https://github.com//openjournals/joss-reviews/issues/7545) in [openjournals/joss-reviews](https://github.com//openjournals/joss-reviews)\n3. 🎉 Merged PR [#30](https://github.com//Juke34/AliNe/pull/30) in [Juke34/AliNe](https://github.com//Juke34/AliNe)\n4. 🗣 Commented on [#7545](https://github.com//openjournals/joss-reviews/issues/7545) in [openjournals/joss-reviews](https://github.com//openjournals/joss-reviews)\n5. 🗣 Commented on [#7545](https://github.com//openjournals/joss-reviews/issues/7545) in [openjournals/joss-reviews](https://github.com//openjournals/joss-reviews)\n\u003c!--END_SECTION:activity--\u003e\n\n\u003c/details\u003e\n\n---\n\n\u003c!--\n**Juke34/Juke34** is a ✨ _special_ ✨ repository because its `README.md` (this file) appears on your GitHub profile.\n\nHere are some ideas to get you started:\n\n- 🔭 I’m currently working on ...\n- 🌱 I’m currently learning ...\n- 👯 I’m looking to collaborate on ...\n- 🤔 I’m looking for help with ...\n- 💬 Ask me about ...\n- 📫 How to reach me: ...\n- 😄 Pronouns: ...\n- ⚡ Fun fact: ...\n--\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fjuke34","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjuke34%2Fjuke34","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fjuke34/lists"}