Sequence tables

A sequence table is like an OTU table except that every sequence gets its own line. (This is the same as 100% identity OTUs.)

Making a sequence table

You'll need to have a fasta file q.fst and a dereplicated fasta q.derep.fst. The output table will have rows in abundance order with labels that correspond to the ones in the dereplicated fasta file.

(Maybe in a future version you could make the seq table using a dereplicated fasta and an index file.)

Example pipelines

Say you have a fasta q.fst but no dereplicated fasta and you want to assign greengenes taxonomies. Then call

/path/to/SmileTrain/otu_caller.py --dereplicate --seq_table --seq_tax

Note that seq_tax is a little experimental right now.