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Pacbio hifi 16s

PacBio HiFi 16S

Data Type

In addition to short read sequencing on the Illumina platform, the PacBio platform can be used to generate long HiFi reads that cover a very large portion of the microbial 16S rRNA gene. These long sequences can be used to identify bacteria from complex mixtures with a much higher degree of taxonomic specificity than short read sequencing.

The analysis of PacBio HiFI 16S data is performed on Cirro using a workflow developed by PacBio which employs the industry-standard tools DADA2 and QIIME2.

nf-core/ampliseq

Supports combining input datasets in a single analysis.

Parameters:

  • Forward Primer Sequence (default: AGRGTTYGATYMTGGCTCAG)
  • Reverse Primer Sequence (default: AAGTCGTAACAAGGTARCY)
  • Filter Quality Threshold (Filter input reads above this Q value)
  • Minimum Quality (Reads with any base lower than this quality score will be removed)
  • Minimum Length (Sequences shorter than this will be discarded)
  • Maximum Length (Sequences longer than this will be discarded)
  • Maximum Expected Errors (Reads with number of expected errors higher than this value will be discarded)
  • Pooling Method (QIIME 2 pooling method for DADA2 denoising)
  • Max Reject (QIIME 2 max-reject parameter for VSEARCH taxonomy classification method)
  • Max Accept (QIIME 2 max-accept parameter for VSEARCH taxonomy classification method)
  • Minimum Identity (Minimum identity to be considered as hit)
  • Minimum Counts per ASV (Total counts of any ASV across all samples must be above this threshold to be retained)
  • Minimum Samples per ASV (Minimum number of samples that an ASV must be found in to be retained)

Workflow Repository: github.com/PacificBiosciences/HiFi-16S-workflow