Research Object Crate for SAMBA: Standardized and Automated MetaBarcoding Analyses workflow

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 produces a full dynamic HTML report including resources used, commands executed, intermediate results, statistical analyses and figures. The SAMBA pipeline can run tasks across multiple compute infrastructures in a very portable manner. It comes with singularity containers making installation trivial and results highly reproducible.

Author

Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric

License

MIT

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