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WigeoN - Online in the Cloud

Run WigeoN in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command WigeoN that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


wigeon - reimplementation of the Pintail 16S DNA anomaly detection utility

DESCRIPTION


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.

OPTIONS


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

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