wigeon (1)

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.

Required:

--query_NAST

multi-fasta file containing query sequences in alignment format

Optional:

--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.