I got a lot of problems trying to convert output of mothur classify.seqs to BIOM format so that I can import data into phyloseq R package. I have FASTA file with paired-end reads already being merged with PEAR program.
I aligned my sequences to SILVA database with this command
mothur > align.seqs(fasta=sample.fasta, reference=silva.bacteria.fasta, processors=4, flip=t)
and then I classified it using the same database
mothur > classify.seqs(fasta=sample.align, reference=silva.bacteria.fasta, taxonomy=silva.bacteria.silva.tax, cutoff=80)
After this procedure I got different files: "sample.summary", "sample.silva.wang.taxonomy" and "sample.silva.wang.tax.summary". But I don't know how to import them into phyloseq R package.
I've read here https://github.com/joey711/phyloseq/issues/245 about shared file from which I can create BIOM file, but I don't have .list or .group files for make.shared command.
Can someone help?