treangenlab / emu Goto Github PK

Hi,
we are currently using the UNITE general fasta v8.3 fungi pre-built database provided here and have been wondering whether there will be an update of it available in the near future?
Best,
Monika

Hi, this morning I was reading over your instructions and then I noticed that the keep counts option outputs: Estimated counts".

Could you explain what is happening with the abundances, when it is not real counts by estimated counts? Does that mean that you take the relative abundances and calculate back what the number of reads for a percentage is, for each sample?

Thank you very much for this nice tool!
If I understand correctly, Emu does not apply a lowest common ancestor (LCA) like approach, right? This was not entirely clear for me when reading the paper.

For instance, when Kraken2 cannot confidently assign a sequence to a species level, it will assign it to the lowest taxonomic rank possible, which is usually the genus level.

Cheers,
Paul

Dear Authors (of Emu):

I am using Emu pipeline on some of Illumina based FASTQ files which are short read. Emu defines that it can run on short read sequences as well by introduction of --type sr command line.

I wanted to know what is the range of short read (base pairs) Emu could act on ?

Is Emu compatible with short read sequencing data of Illumina ? then of what range (base pairs)

Regards
Arpit

Hello,

Great tool! I just wanted to bring to your attention something I learned recently: minimap2 does not report secondary alignments for short reads by default when using the -x sr preset, unless you set --secondary=yes. See lh3/minimap2#846. I know Emu is designed primarily for long reads, but presumably this would impact the short read option.

-David

Emu has a default minimum abundance. Wanted to know if you have any data to show that to what extent we could lower the minimum abundance score. I have kept it to 10 (to the power of -8). If we lower the minimum abundance score to even lower levels will we be able to get more species in our list ?

Secondly, I wanted to know which is the recommended amount of reads that a stool profile should give in order to get a good idea of the gut microbial spectrum in the sample. Our sample is giving around 30-35K reads from the Nanopore Flongel flow cell.

Lastly wanted to inquire, at what minimum reads does the emu pipeline detect a species ? Is there a way we could set our own threshold of min reads for a species to be detected ?

Please help in the regard