Hi everyone, Is there a pipeline to perform 16S metagenomic long read analysis ?
My data look like :
zcat in00345_1V1V9.fastq.gz | head
@m64524e_241022_205042/2/ccs/9839_11335
GGTTTGATC
I use the last version of QIIME2
Hi @Hongo,
Welcome to the :qiime2: forum!
The main support that we have for PacBio CCS (it looks like that's what you're using here - please correct me if I'm wrong) is in the q2-dada2 plugin - see the denoise-ccs action. Before running that, you'll need to import your data into a SampleData[SequencesWithQuality] Artifact. If your sequence data is demultiplexed (one sample per fastq.gz file), the fastq manifest format is likely the best one to use for importing (see here). If it's still multiplexed, one of the other formats for sequence data with quality information will be the most relevant, but I'm not sure which offhand.
After you've successfully run denoise-ccs most of the downstream steps should be the same as for Illumina data, so referencing the Moving Pictures tutorial is likely the best place to start.
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