Hi, would like to use Galaxy to build an eDNA workflow pipeline to process Metabarcoding data from Illumina. Is this possible or are there other open source tools available to do this ?
Basic steps needed :
Read demultiplexed FASTQ files
Merge paired reads
Filter and trim
Cluster
Map to BINs in BOLD or another database
Outputs taxa lists for each sample.
We have some community tutorials here that can get you started. Many will have a workflow template that you could build on, or these can at least serve as examples.
If you are new to Galaxy, this my favorite simple tutorial to start with.
You could also explore through a learning pathway. These will quickly get you oriented then go in for a deeper scientific tool exploration.
Please let us know if you need more help! I think everything you listed should be possible. 
⅕Thanks Jennifer and Galaxy support team,
I am quite new to DNA. Completely self taught. But have made a lot of progress in 18 months.
I think open access science is fantastic. I currently use mBRAVE. I don’t know if Galaxy is right tool for what I do but happy to find out and share feedback.
Feel free to mention AquaTerra to anyone in California who might want to get involved !!!
Adam
Admin-redacted: privacy
Great, glad you are exploring! For anyone else reading, this is one of the workflows in the Ecology group posted above. Maybe useful for comparisons between methods.
Thanks!
Hi @Adam_Hillier ,
Thank you for exploring Galaxy solutions for eDNA analysis! And big thank you @jennaj for precise informations related notably to the work we are doing thanks to the Galaxy Ecology initiative! I think of interest to add links to these Galaxy training materials dedicated to metabarcoding, as you can see that aside of obitools, there is others toolsuite in Galaxy to deal with eDNA analysis as mothur, qiime and dada2. One can also mention that many others Galaxy tools can be used for eDNA analysis as Blast related tools or generic DNA sequence treatment tools (notably for reading demultiplexing FASTQ files or Filter and trim).
Please, don’t hesitate to come back to us if more information / help is needed!