Academic Journal
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
| العنوان: | BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons |
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| المؤلفون: | Djemiel, Christophe, Dequiedt, Samuel, Karimi, Battle, Cottin, Aurélien, Girier, Thibault, El Djoudi, Yassin, Wincker, Patrick, Lelièvre, Mélanie, Mondy, Samuel, Chemidlin Prévost-Bouré, Nicolas, Maron, Pierre-Alain, Ranjard, Lionel, Terrat, Sébastien |
| المساهمون: | Agroécologie Dijon, Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté COMUE (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011) |
| المصدر: | ISSN: 1471-2105 ; BMC Bioinformatics ; https://institut-agro-dijon.hal.science/hal-03014150 ; BMC Bioinformatics, 2020, 21 (1), pp.1-21. ⟨10.1186/s12859-020-03829-3⟩. |
| بيانات النشر: | HAL CCSD BioMed Central |
| سنة النشر: | 2020 |
| المجموعة: | Université de Bourgogne (UB): HAL |
| مصطلحات موضوعية: | Ecology, Metabarcoding, Bacterial, Archaeal, Fungal, Photosynthetic microeukaryotes, ReClustOR, France, Land-use, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
| الوصف: | International audience ; Background: The ability to compare samples or studies easily using metabarcodingso as to better interpret microbial ecology results is an upcoming challenge. A grow‑ing number of metabarcoding pipelines are available, each with its own benefts andlimitations. However, very few have been developed to ofer the opportunity to charac‑terize various microbial communities (e.g., archaea, bacteria, fungi, photosyntheticmicroeukaryotes) with the same tool.Results: BIOCOM-PIPE is a fexible and independent suite of tools for processing datafrom high-throughput sequencing technologies, Roche 454 and Illumina platforms,and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeu‑karyote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1)remove chimeras based on read abundance, (2) align sequences with structure-basedalignments of RNA homologs using covariance models, and (3) a post-clustering tool(ReClustOR) to improve OTUs consistency based on a reference OTU database. Thecomparison with two other pipelines (FROGS and mothur) and Amplicon SequenceVariant defnition highlighted that BIOCOM-PIPE was better at discriminating land usegroups.Conclusions: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and23S rRNA genes in the same packaged tool. The new post-clustering approach defnesa biological database from previously analyzed samples and performs post-clusteringof reads with this reference database by using open-reference clustering. This makes iteasier to compare projects from various sequencing runs, and increased the congru‑ence among results. For all users, the pipeline was developed to allow for adding ormodifying the components, the databases and the bioinformatics tools easily, givinghigh modularity for each analysis. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | hal-03014150; https://institut-agro-dijon.hal.science/hal-03014150; https://institut-agro-dijon.hal.science/hal-03014150/document; https://institut-agro-dijon.hal.science/hal-03014150/file/s12859-020-03829-3.pdf; PUBMEDCENTRAL: PMC7603665; WOS: 000588098400003 |
| DOI: | 10.1186/s12859-020-03829-3 |
| الاتاحة: | https://institut-agro-dijon.hal.science/hal-03014150 https://institut-agro-dijon.hal.science/hal-03014150/document https://institut-agro-dijon.hal.science/hal-03014150/file/s12859-020-03829-3.pdf https://doi.org/10.1186/s12859-020-03829-3 |
| Rights: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.1486A028 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1186/s12859-020-03829-3 |
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