ozagordi
commented
7 years ago Hi.
I would say you need to look into amplian.py for directions. It makes some preprocessing and then calls diri_sampler for the error correction. diri_sampler takes a multiple alignment in fasta format and runs the clustering. The output is split over several files, but you are probably mostly interested in the file *cor.fas, that contains the haplotypes in fasta format. Does this help?
greenstick
I'm interested in using only the error correction procedures in ShoRAH for an analysis. To do this, I would need to input either FASTQ or BAMs into ShoRAH's error correction algorithm, and receive a similar output with corrected reads. If a simple transformation is required I could code one up.
Looking at the source and documentation, it doesn't look like this is possible without forking and writing a use case specific implementation. Before going down that road, I thought it best to ask: Is there an established way to run ShoRAH's error correction as a standalone process?
Thanks