KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies)

Abstract Summary Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a ‘one health’ approach, for a better comprehension and surveillance of humans, plants or animals’ health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to ‘omics’ data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated ‘Galaxy KaruBioNet’ platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html Contact dcouvin@pasteur-guadeloupe.fr Supplementary information Supplementary data are available at Bioinformatics Advances online.

[1]  Nalin Rastogi,et al.  SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis , 2022, Database J. Biol. Databases Curation.

[2]  D. Meyer,et al.  Critical Evaluation of Cross-Sectoral Collaborations to Inform the Implementation of the “One Health” Approach in Guadeloupe , 2021, Frontiers in Public Health.

[3]  Y. Reynaud,et al.  Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies) , 2021, Frontiers in Microbiology.

[4]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[5]  Nalin Rastogi,et al.  MTBCtools: a non-exhaustive list of software tools/resources for bioinformatics analyses of Mycobacterium tuberculosis complex, the causative agent of tuberculosis , 2021 .

[6]  Michael Y. Galperin,et al.  COG database update: focus on microbial diversity, model organisms, and widespread pathogens , 2020, Nucleic Acids Res..

[7]  Nalin Rastogi,et al.  Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families , 2020, Database J. Biol. Databases Curation.

[8]  D. Meyer,et al.  The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis , 2020, bioRxiv.

[9]  Andrew J. Page,et al.  Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru , 2020, bioRxiv.

[10]  Cheng Yee Tang,et al.  MIRUReader: MIRU-VNTR typing directly from long sequencing reads , 2019, Bioinform..

[11]  Sean Kennedy,et al.  SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis , 2019, BMC Bioinformatics.

[12]  Z. Iqbal,et al.  Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe , 2019, Wellcome open research.

[13]  Nalin Rastogi,et al.  Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. , 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[14]  Jim F Huggett,et al.  Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs , 2019, Genome Medicine.

[15]  Olivier Gascuel,et al.  NGPhylogeny.fr: new generation phylogenetic services for non-specialists , 2019, Nucleic Acids Res..

[16]  Christophe Noroy,et al.  Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria , 2019, PLoS Comput. Biol..

[17]  Xingang Wang,et al.  RaGOO: fast and accurate reference-guided scaffolding of draft genomes , 2019, Genome Biology.

[18]  Jian Yang,et al.  VFDB 2019: a comparative pathogenomic platform with an interactive web interface , 2018, Nucleic Acids Res..

[19]  Keith A Jolley,et al.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.

[20]  James Robertson,et al.  MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies , 2018, Microbial genomics.

[21]  Manzour Hernando Hazbón,et al.  Mycobacterial biomaterials and resources for researchers , 2018, Pathogens and disease.

[22]  Marius van den Beek,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update , 2018, Nucleic Acids Res..

[23]  Alessandra Carbone,et al.  Meet-U: Educating through research immersion , 2018, PLoS Comput. Biol..

[24]  Mahendra Mariadassou,et al.  FROGS: Find, Rapidly, OTUs with Galaxy Solution , 2018, Bioinform..

[25]  J. Deloumeaux,et al.  Building a Network of Biological Resource Centers for Research Purposes in the Caribbean: Excellent Potential for Research into Public Health Diseases , 2017 .

[26]  C. Berg,et al.  A Comparison of Three Holistic Approaches to Health: One Health, EcoHealth, and Planetary Health , 2017, Front. Vet. Sci..

[27]  Nalin Rastogi,et al.  SpolSimilaritySearch - A web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex. , 2017, Tuberculosis.

[28]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[29]  Y. Teo,et al.  SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads , 2016, Genome Medicine.

[30]  Özlem Tastan Bishop,et al.  H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa , 2016, Genome research.

[31]  outh Green collaboratorsa.  The South Green portal : a comprehensive resource for tropical and Mediterranean crop genomics , 2016 .

[32]  Thomas Abeel,et al.  Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal , 2015, PLoS medicine.

[33]  Andrew J. Page,et al.  Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.

[34]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[35]  Ole Lund,et al.  In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.

[36]  Heng Li,et al.  Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..

[37]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[38]  Emmanuel Albina,et al.  Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context , 2013, Nucleic acids research.

[39]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[40]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[41]  Nalin Rastogi,et al.  SITVITWEB--a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. , 2012, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[42]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[43]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[44]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[45]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[46]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[47]  Domenica D'Elia,et al.  The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community , 2009, BMC Bioinformatics.

[48]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[49]  Jean-Michel Claverie,et al.  Phylogeny.fr: robust phylogenetic analysis for the non-specialist , 2008, Nucleic Acids Res..

[50]  Julio Collado-Vides,et al.  Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet). , 2002, Applied bioinformatics.

[51]  Padhraic Smyth,et al.  Knowledge Discovery and Data Mining: Towards a Unifying Framework , 1996, KDD.