Compare bioinformatics pipelines

iobis / pacman

PacMAN data management issues and action items

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Compare bioinformatics pipelines #7

Open SSuominen1 opened 3 years ago

SSuominen1 commented 3 years ago

[x] Pema (ARMS)
[x] QZIP (AWI)
[x] Tourmaline (NOAA)
[x] Banzai (MBON)
[x] ANACAPA (UCLA)
[x] SLIM (University of Geneva)
[x] CASCABEL (NIOZ)
[x] ABYSS (Ifremer)
[x] MgNIFY (ENA)

In collaboration with the GLOMICON initiative?

SSuominen1 commented 3 years ago

Comparisons of the pipelines can be found in the BioinformaticsPipeline document here in the repo. PacMAN should probably adopt an existing pipeline (using dada2 for ASV inference), and develop a version where the users can just upload their data to run the analysis. Out of these pipelines ANACAPA is developed for a large eDNA project, and could be suitable for our purposes as well.

Does GLOMICON currently have any initiatives regarding bioinformatic pipelines/information?