For single end Demultiplexed sequence data, when prepare manifest, do we need direction?

[CamilleZhao]

For single end Demultiplexed sequence data, when prepare manifest, do we need direction?

sample-id absolute-filepath
sample-1  /scratch/microbiome/sample1_R1.fastq.gz
sample-2  /scratch/microbiome/sample2_R1.fastq.gz

[lizgehret]

Hi @CamilleZhao,

Happy New Year

You do not need to specify forward-absolute-filepath and reverse-absolute-filepath for single end data. The format that you have above is exactly correct! You can check out our docs on formatting your manifest file here if you want any additional examples.

Cheers

[CamilleZhao]

Happy new year and thank you for the quick response.

It is actually the first time that I am trying to analysis Nanopore full-length 16S. May I know if qiime2 can work on the Nanopore full-length 16S? If yes, may I know if any protocol that I can follow?

[lizgehret]

Hi @CamilleZhao,

The short answer is technically yes, but it also depends on what exactly you're trying to accomplish- here are a couple of good threads from other folks who were working with full-length Nanopore 16S data and what they did in QIIME 2 vs. other tools:

Nanopore Long Read Demultiplexed Full 16S rRNA Seq

Hello, I'm new here and had a few questions. So the lab I'm working in doesn't have a bioinformatician, so I've taken that role and have been learning on the fly. So I did the sequencing using the 16S Barcoding Kit 24 V14 (SQK-16S114.24) protocol and the MinION MK1C sequencing device. I selected the super high accuracy base caller, demultiplexed it, and trimmed the adapter/primers using guppy (v6.3.8). After that, I filtered based on length and quality using chopper. Everything up to here was fi…

16S full length nanopore to ASVs (new approach?)

Hi everybody, I am new here and I have no better idea than to do something crazy. I have no idea if it is possible due to the fact of the sequencing nature. But could I map ASV reference sequences produced by QIIME2 into 16S full-length nanopore sequences? Both the Illumina (MiSeq 2 × 250 paired-end) and nanopore sequencing were made with soil samples. My final goal is to produce an ASV ID abundance table with the nanopore data. So as to "compare" the samples sequenced with Illumina with the n…

Hope this helps!

Cheers