wigeon - reimplementation of the Pintail 16S DNA anomaly detection utility
WigeoN examines the sequence conservation between a query and a trusted
reference sequence, both in NAST alignment format. Based on the sequence
identity between the query and the reference sequence, there is an expected
amount of variation among the alignment. If the observed variation is greater
than the 95% quantile of the distribution of variation observed between
non-anomalous sequences, then it is flagged as an anomaly.
WigeoN is a flexible command-line based reimplementation of the Pintail
algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36.
WigeoN is useful for flagging chimeras and anomalies only in near full-length
16S rRNA sequences. WigeoN lacks sensitivity with sequences less than 1000 bp.
To run WigeoN, you need NAST-formatted sequences generated by the nast-ier
utility.
WigeoN is part of the microbiomeutil suite.
- --query_NAST
- multi-fasta file containing query sequences in alignment
format
- --db_NAST
- db in NAST format
- --db_FASTA
- db in fasta format (megablast formatted)
- --num_top_hits
- default 1: uses only the single best match.
- --plot
- --DEBUG
- --exec_dir
- cd to exec_dir before running
http://microbiomeutil.sourceforge.net/#A_WigeoN
This manual page was written by Andreas Tille <
[email protected]> but can
be freely used for any other distribution.