Hi Daniel,
Thanks a lot for your awesome tool, Megan is fantastic.
I used a lot the diamond-megan pipeline for analyzing metagenomic short reads, but now I’m interested in a pipeline using blastn.
Could you gently write, as you did it for the diamond-megan pipeline, a general workflow?
Thank you in advance,
Cheers,
Lapo
Dear Lapo,
you first run the reads through blastn, saving the alignments using pairwise format, also known as format 0.
Then, use the tools/blast2rma program to compute an RMA file from your fasta file and blastn output file. Run the program without any options to see a help listing.
If the reference sequence header lines contain organism names, then you can use the “taxon name parsing” option to identify taxa. Otherwise, you should supply this mapping file: megan-nucl-Jan2021.db.zip
Aligning against a DNA database will only assign your reads against taxa, not genes. Take a look at the AADDER program that comes with MEGAN if you are interested in trying to also bin reads by genes. We haven’t published it yet, but I’d be happy to help you to get it to work on your data, if this is what you need.