Shoreline data without primers appear to be in either orientation

[cjfields]

We have recent Shoreline data that (having been demultiplexed through SBAnalyzer) appear to be in mixed orientation. This is partially dealt with when classifying reads when using assignTaxonomy in the workflow as it uses the tryRC flag, but the posted sequences are still in mixed orientation which will lead to erroneous results with any phylogenetic analyses.

[cjfields]

This may be due to the input data not being properly reoriented within Shorelines's SBAnalyzer. I'm assessing this at the moment with some example data.

[cjfields]

The workflow will have to require that input data from Shoreline (either StrainID or the standard 16S) need to retain the primers so that the trimming step can also be used for reorienting them. SBAnalyzer has this option.

[cjfields]

Some initial code for this has been added to the repo, but we will need to add some documentation re: any Shoreline data inputs to mention they will either require being pre-trimmed and reoriented, or will require primers (whereupon the standard steps can reorient them).

[cjfields]

This essentially works fine with the caveat that the reads need to be demultiplexed with Shoreline tools while keeping primers intact (so the workflow can readily detect and reorient the reads accordingly). Saying that, we do not expect to add additional functionality for this due to Shoreline Biome's rebranding as Intus Bio and removal of their StrainID kits for sample preparation, with a move to end-to-end (seq to results) in-house microbiome characterization.

[cjfields]

This is of low priority due to the inavailability of the Shoreline kit, though we do expect other long read amplicons similar to Shoreline to require reorienting.