SeBiMER

SeBiMER

IFREMER Bioinformatics Core Facility

SeBiMER

SeBiMER is the Bioinformatics Core Facility of IFREMER, the French National Institute for Ocean Science.

SeBiMER is in charge of providing a large community of marine biologists with all the requirements (knowledge, softwares and data) to handle small and large scale bioinformatics projects, mostly in the fields of metabarcoding (eDNA), (meta-)transcriptomics and genomes assembly & annotaton.

SeBiMER manages two Galaxy portals and more than 500 softwares covering 28 EDAM Operation topics, all of them being deployed and configured on DATARMOR, Ifremer’s supercomputer. SeBiMER is also in charge of managing sequencing data in a FAIR way on behalf of biologists: data is organized using EDAM ontology, stored on high-performance and secured disk storage and made accessible to 11,000 cores of DATARMOR.

SeBiMER team is made of 5 permanent engineers and PhDs with extensive skills in biology, bioinformatics, computer science, software development, data analysis.

SeBiMER missions

SeBiMER activity targets 5 main missions :

  • IT managment (e.g. sequencing data and software installation & configuration on DATARMOR);
  • Bioanalysis (e.g. extensive data analysis in close relation with research teams);
  • Software Development (e.g. design of new tools and data analysis workflows; see below);
  • Bioinformatics R&D
  • trainings

Visit our institutional web site for more information.

SeBiMER softwares

Find here some of our free and open source projects.

SAMBA

SAMBA is a Nextflow based metabarcoding data analysis workflow. View SAMBA example report.

ORSON

ORSON is a Nextflow based for proteome and transcriptome functional annotation.

ToolDirectory

ToolDirectory is a dynamic software catalogue viewer. View ToolDirectory at work!

BeeDeeM

BeeDeeM is a bioinformatics databank manager.

BlastViewer

BlastViewer is a graphical tool to handle analysis BLAST, PLAST or Diamond results. Also capable of importing InterproScan results.

More softwares

All our softwares and pipelines are freely available on Ifremer Gitlab server, as well as on Github.