Aligned sequences and Rescript

[Nicholas_Bokulich]

Hello @jwdebelius!

@jwdebelius

I’m trying to figure out how aligned sequences line with with rescript

In general, the degap-seqs method is in there to handle aligned sequences, so you are correct the workflow would be something like: import aligned seqs --> degap --> do whatever.

Unfortunately, that method only degaps aligned DNA sequences... although RESCRIPt defines an RNASequence type, we still need to add an AlignedRNASequence format

@jwdebelius

Do I just download them from the SILVA 138 release and then

In the case of SILVA, you can just use the unaligned sequences — right? — in the case of SILVA you can also use the get-silva-data pipeline to reduce your blood pressure, which downloads and imports/formats the SILVA sequences and taxonomy.

See "getting SILVA data the easy way", by @SoilRotifer:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…

As far as I know, there are aligned and unaligned versions for the various SILVA releases. It would be neat to get more support for aligned sequences in there for other datasets and to support streamlined integration with plugins that use aligned reference sequences. Any interest in contributing a "good first issue" to RESCRIPt?

@jwdebelius

Sorry if this is super naive.

Not at all... maybe what you'd call a documentation hole.
Besides, I'm just glad RESCRIPt is getting the attention!