Hello, I am currently performing 16S rRNA amplicon metagenomic analysis using the ONT platform through the EPI2ME workflow with the Minimap2-based taxonomic classification approach. I have successfully completed the analysis pipeline. However, I could not obtain the representative sequence FASTA files, which are required for downstream functional prediction using PICRUSt2.
Could you please advise how to retrieve the aligned or representative sequence FASTA/FASTQ files from the EPI2ME workflow outputs? Alternatively, if this workflow does not generate representative sequences suitable for PICRUSt2, could you recommend an appropriate workflow or approach to obtain them?
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written
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Ramen •
2 answers
If you really need a workflow that generate a rapresentative sequence you can try laca (https://github.com/yanhui09/laca; manuscript:https://pmc.ncbi.nlm.nih.gov/articles/PMC12160608/) or similar.
Good luck!
I have been dealing with the same situation and found laca (https://github.com/yanhui09/laca) and NanoASV (https://github.com/ImagoXV/NanoASV) quite useful.
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Looking at the workflow it looks like the default option produces abundance table and some plots. You can get assignments of individual sequences using (
include_read_assignments) option as a TSV file.That said, you could choose the option to keep the BAM file after alignment and generate a consensus sequence.
Thank you for your prompt and proactive response. I tried the script mentioned below, which also includes the include_read_assignments option. For your convenience, I have attached a screenshot of the output directory along with the TSV file generated using the include_read_assignments option.