rtax - Rapid and accurate taxonomic classification of short
paired-end sequence reads from the 16S ribosomal RNA gene
- -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
A quickstart example can be found here:
https://github.com/davidsoergel/rtax/wiki/QuickStart
Rtax can also be used within QIIME workflows, see this link
for more information: http://www.qiime.org/tutorials/rtax.html
This manual page was written by Simon Kainz
<simon@familiekainz.at> for the rtax package.
Rtax was written by David A. W. Soergel
<soergel@cs.umass.edu>.