I'm working with MISeq processed sequences of microbiome 16s samples. Is there any reason why I should use R tools like
msa (Bioconductor) or
decipher over NGS tools like
Specifically, I'm using a dada2 workflow put out by the authors. My goal is the produce the
phyloseq object for downstream analysis.
In this section
they construct a phylogenetic tree using
phangorn. But first, they use DECIPHER for the multiple sequence alignment.
For certain reasons I'd like to do this without
DECIPHER. Also, although this sounds lame, I don't want to become an expert in MSA as this is a very tiny part of the workflow, but is a bottleneck for generating the tree. My background is more in whole-genome sequencing like ChIP- and RNA-Seq.
So, can I use
STAR for MSA?