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Welcome on the website on the CNR "Antibiotic Resistance" French Reference Center database provides by the CNR
"Antibiotic Resistance" at Clermont-Ferrand, France.
This website provide an interface to our home "Antibiotic Resistance" database for health watchfulness and research purpose on the antibiotic resistance in France
You can access of our public data or data which you have right access.
Contact-us for further information.
The current date in France : 27 novembre 2024 17:36 (UTC)
This website provide an interface to our home "Antibiotic Resistance" database for health watchfulness and research purpose on the antibiotic resistance in France
| Version | Date | Comment |
|---|---|---|
| 41 | 12/06/24 | Refit many pipelines with long-read data. Add DNS 'basav-ngs.fr'. Minor fixes. |
| 40 | 08/04/24 | Add Pacbio format sequence available in the CNR database. |
| 39 | 19/03/24 | Add new job name. |
| 38 | 27/02/24 | Add new strain class tag. Add nanopore taxonomy options. Minors fixes. |
| 37 | 08/12/23 | rework name on job to hpc2. add s3 transition code. minors fix. |
| 36 | 11/10/23 | Add SPATyper and SCCmecFinder CGE tools. Begin bricks of translation to s3 system. |
| 35 | 04/09/23 | Rework/optimization database structure on gene information storage. Add warning column on wiki gene page. |
| 34 | 08/08/23 | Rework some visual parts of the website. Add graphic for clonal group. Change and rework 'Annotation PAO' pipeline to 'Annotation Besancon' pipeline. |
| 33 | 02/05/23 | Add first implementation of group clonal base on CHEWBBACA (server side) and Message (Server-User) system. Many Fixes. New taxonomic database. |
| 32 | 17/04/23 | Add first implementation of ChewBBACA tools on the website. Many fixes. |
| 31 | 03/04/23 | Add more improvement on priority stats part of the website (add running tasks time side). Add antibiotic filter on main table.Add more pipeline for the nanopore data (still work to do on this part). |
| 30 | 25/02/23 | Add priority job manager inside website. Add possibility to treat nanopore sequence. Rework interface. |
| 28 | 15/11/22 | Improvement of wiki gene section. Add map for strain classe. Add department code filter. |
| 27 | 07/11/22 | Rework some graphical interface of the website. Others minors improvement. |
| 26 | 11/10/22 | Rework Import sequence part of the website. Add few improvement in many parts of the site. Add TreeTime at the PhyloTree-SNP pipeline. |
| 25 | 14/08/22 | Small Rework in wiki strain page. Rework upload page. |
| 24 | 02/08/22 | Add MGEFinder of CGE for pipeline. Rework Mutation database side of the website. |
| 23 | 11/07/22 | Add color for reads quality and assembly quality. Add version 2 of taxonomy database. Add correction in SNP pipeline for case with QMAP below 60. |
| 22 | 16/05/22 | Rework monitor jobs view. Others minors update. |
| 21 | 15/04/22 | Rework visual on wiki strain page (color). Add the tree choice during the launch page of phylotree SNP and the choice to edit the phylotree name. |
| 20 | 16/03/22 | Rework MLST score render in case of multiple alleles found. Add filter on strain classification in general table page. |
| 19 | 21/02/22 | Global update of the website. Rework of statistics tasks. Now the waiting task are not display in the main table. |
| 18 | 02/12/21 | Rework Database for Mutation and sequence organization. If your strains are not analyse on the version 92 or higher of the ARM database version, please re-analyse them with the SeqDetector pipeline. |
| 17 | 26/10/21 | Add new statistics view of strains by site. Now the total selection of strains in the general table show the number of strains. |
| 16 | 07/10/21 | Add new option in general table. Add molecular antibiotic information. Rework mutation visual. |
| 15 | 07/09/21 | Add the work of our IT internship of this summer (Mateo HIRIART) --> Add Auract program at the end of the SNP pipeline and add microreact and Auspice visual link. Minor Optimization. |
| 14 | 22/07/21 | Add multi-fasta function in alignment page. Rework selection of gene&mutation element to the strain report. Add 'Div' class to few uncertain genes. |
| 13 | 02/07/21 | Rework Report strain document for the Rennes staff need. Add alignment feature in wiki strain page. Add all gene with mutation model in wiki strain page in specific table. Add combination cgMLST for A.baumannii. |
| 12 | 02/06/21 | Rework Report strain document. Rework Mutation information. Add Genotype Resistance Information for Beta-lactam |
| 11 | 25/05/21 | Add possibility to analyse only 2 strains with the SNP-Phylotree pipeline (No tree will be produced with this configuration). Add label class for strain. Add possibility user to define strains in few working class (expertise, study, research and other). Add possibility to add GLIMS ID to a strain (this id can be used to produce barcode in strain report). Important rework of the strain report. |
| 10 | 30/04/21 | General Improvement. Add document for SNP-Phylotree. Rework Mutation database. Now mutation described on a known mutation resistant position are properly saved (A200[G]). |
| 9 | 19/04/21 | Improvement visual. Rework of the 'SNP-Detection' pipeline with new parameters editable. |
| 8 | 01/04/21 | Improvement visual. Add more statics graphs. Now some fields in filters of the main table are hide by default. You can now rename phylotree done with [phyloTree] pipeline. Rework Fastq Import page with a verification step before the fill of the database. |
| 7 | 18/03/21 | Add Pipeline [Extra Detection]. This pipeline is a mirror pipeline of [Detection] but with lower threshold of coverage (70%->40%) and identity (70%->40%). The result are not store in the CNR Database. The result are only available in the report to download in strain wiki page ; The genomes reference database is updated and cleaned with new genomes. |
| 6 | 23/02/21 | Update Assembly pipeline with new assemblers (all assemblers available in Shovill (spades, skesa, velvet, megahit)). Shovill-Spades replace SKESA in default assembler. Test at import of corrupted read gzip file. Now, you can change the species name for multiples strains. The low coverage base for SNP detection is now display in the SNP-detection table. |
| 5 | 05/02/21 | Rework Pipeline PAO; A new Job-Queue is defined for upload sequence; The number of simultaneous jobs has been lowered to ensure a better website performance. The pipeline [Taxonomy-plasmid] and [PlasmidFinder] are now in automatic mode in the upload step; Others minors improvements |
| 4 | 28/01/21 | Rework filter part on species name; Rework PlasmidID and plasmidTaxonomy part on wiki-strain page; Rework PAO pipeline; Now re-processing Assembly step for strain no longer suppress readmapper result |
| 3 | 19/01/21 | Add Plasmid Centrifuge Database; Add PlasmidID new database; Add Plasmid Taxonomy Centrifuge Tool; Rework Main Database filter; Other minors improvements. |
| 2 | 14/11/20 | Add View Combination for CG-MLST; Update Annotation-PAO Pipeline; Optimisation of [SNP-Detection] pipeline; Add Antibiotics information in Upload and view in wiki [Strain] |
| 1 | 07/10/20 | Initialization version log |
| Version | Date | Comment |
|---|---|---|
| 21 | 04/06/24 | Version 104 of ARM database and version 41 of VIR database. NDARO update + others updates. |
| 20 | 17/01/24 | Version 9 of the taxonomic database. |
| 19 | 12/05/23 | Version 102 of ARM database and version 40 of VIR database. NDARO update + others updates. |
| 18 | 01/08/22 | Version 100 of ARM database. Rework tem_promoteur model. |
| 17 | 25/07/22 | Version 99 of ARM database. Rework some genes like tet(d). |
| 16 | 21/07/22 | Version 98 of ARM database. Add mutations for temp promoter. |
| 15 | 02/05/22 | Version 96 of ARM database and 38 of VIR database. Update NDARO and Mutation form PointFinder. |
| 15 | 12/05/22 | Version 97 of ARM database. Update oprD gene variants. |
| 14 | 29/03/22 | Version 94 of ARM database. |
| 13 | 24/03/22 | Version 93 for ARM database. |
| 12 | 02/12/21 | Version 92 for ARM database. |
| 11 | 07/10/21 | Version 91 for ARM database. |
| 10 | 14/09/21 | Version 90 for ARM database and Version 37 for VIR database. |
| 9 | 17/06/21 | Version 89 for ARM database (add mecA and refine other genes) |
| 8 | 02/06/21 | Version 86 for ARM database (rework Mutation system + update NDARO + add genotype resistance for beta-lactam) + Version 36 for VIR database. |
| 7 | 30/04/21 | Version 82 for ARM database (rework mutation model and add few ARM gene) |
| 6 | 25/04/21 | Version 81 for ARM and Version 34 for VIR database (sync with last NDARO update; Rework some mutation model and manual add of ARM gene) |
| 5 | 01/04/21 | Version 80 for ARM and Version 33 for VIR database (sync with last NDARO update; rework crpP and agn information). |
| 4 | 02/02/21 | Version 77 for ARM and Version 28 for VIR database |
| 3 | 28/01/21 | Version 76 for ARM and Version 27 for VIR database |
| 2 | 09/12/20 | Version 75 for ARM and Version 25 for VIR database (rework [fos] gene family, re class [leuO] and [mfd] genes) |
| 1 | 07/10/20 | Initialization version log |
You can access of our public data or data which you have right access.
Contact-us for further information.