rtax: Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16s ribosomal rna gene

OPTIONS

-r refd: reference database in FASTA format
-t taxonomy: taxonomy file with sequence IDs matching the reference database
-a queryA: FASTA file containing query sequences (single-ended or read 1)
-b queryB: FASTA file containing query sequences (read b, with matching IDs)
-x: Reverse-complement query A sequences (required if they are provided in the reverse sense)
-y: Reverse-complement query B sequences (required if they are provided in the reverse sense)
-i regex: regular expression used to select part of the fasta header to use as the sequence id. Default: "(\S+)"
-l file: text file containing sequence IDs to process, one per line
-d delimiter: delimiter separating the two reads when provided in a single file
-m tempdir: temporary directory. Will be removed on successful completion, but likely not if there is an error.
-f: for sequences where only one read is available, fall back to single-ended classification. Default: drop these sequences.
-g: for sequences where one read is overly generic, do not fall back to single-ended classification. Default: classify these sequences based on only the more specific read.
-o classifications.out: output path