Hi, I want to use Mothur pipeline with MinION data. Please let me know if it supports and a manual.
Thank you,
I asked roughly that recently, Pat indicated that he thinks the quality still isnt’ good enough. I’m hoping to do a nanopore test run in the next month or so. I’ll try to remember to post back here with what I use.
Mock community data would be fantastic
This run will be mocks and a few samples that have been sequenced to death, including pacbio with the same library prep kit.
Hello!
I am getting interested in this technology.
How did or is the project doing?
Hi @Kendra, I am just following up with this thread, and I am just curious to know how did the project go?
many thanks
Venkat
Hi All. Sorry I dropped the ball on this. I’ve finally gotten my gridion and started sequencing. I have a few zymo mocks sequenced with nanopore’s 16s kit on R9.? (too high error to use mothur), 8f/1391R with nanopore PCR barcoded on R10.4, plus I’ve run them on MiSeq using standard v4 sequencing with EMP version of 515f/806R.
I’m trying to get the R10.4 data through mothur but I’m not super confident it’s going to give me anything useful. There are very few non-unique sequences which suggests too high error rates. This is still running (4 days and counting on 32 cores 500gb ram).
I’ve also pcr.seq selected out just v4 from this data and am trying to run mothur on that section to get a better idea of how this compares to illumina.
Finally, I’m going to repeat both these analyses on just the duplex data which is ~10% of the R10.4 run.
I’m presenting all this at ASM Microbe next month, so I have a deadline to get this done!
Hi. I wonder if a Mothur pipeline for MinION data is available. There are companies providing long reads sequences obtained targeting abeV48A: 515 FB and 1391R primers.
Many thanks!
I tagged you in the thread with my current process for nanopore.
curious who’s offering v4-8? That’s an interesting choice of region.
Hi Kendra,
Thank you for the update on the nanopore reads analysis process.
I learned a company in Denmark is providing v4-8 reads.
Yes, it would be exciting to see how it works…
Hello!
Question:
Is the fastq format directly from the nanopore is not the same that the one from Illumina. I think not because there is an extraline on the fast.q given from nanopore where there are infos about the run and technology used. But I might be mistaken. Can mothur read it correctly?
what’s the extra line? I have my code in the other thread