SeBiMER
OverviewSeBiMER 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, in a broad range of fields such as metabarcoding (eDNA), (meta-)transcriptomics and genomes assembly & annotaton.
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/47
Public web page: https://ifremer-bioinformatics.github.io/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 8th Jul 2021
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https://orcid.org/0000-0002-7139-4073
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
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SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric
Submitter: Cyril Noel
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ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
