SAMBA: Standardized and Automated MetaBarcoding Analyses workflow
Version 1

Workflow Type: Nextflow
Stable

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.

Version History

Version 1 (earliest) Created 10th Sep 2021 at 14:40 by Cyril Noel

Added/updated 2 files


Open master e560923
help Creators and Submitter
Creators
Additional credit

Laure Quintric

Submitter
Citation
Cormier, A., Durand, P., Noel, C., & Leroi, L. (2021). SAMBA: Standardized and Automated MetaBarcoding Analyses workflow. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.156.1
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Views: 876   Downloads: 18

Created: 10th Sep 2021 at 14:40

Last updated: 10th Sep 2021 at 14:43

Last used: 7th Oct 2022 at 12:55

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Total size: 470 KB
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