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cm_to_wigeon - helper for wigeon (Pintail 16S DNA anomaly detection)

CM_TO_WIGEON(1) User Commands CM_TO_WIGEON(1)

NAME

cm_to_wigeon - helper for wigeon (Pintail 16S DNA anomaly detection)

DESCRIPTION

Unfortunately this tools that comes in connection with wigeon(1) is not documented but it regards the options below. If you know better about its purpose please drop us a note using reportbug on your Debian system.

OPTIONS

Required:

--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)

Common options

-n
number of top matching database sequences to compare to (default 15)
-R
min divergence ratio default: 1.007
-P
min percent identity among matching sequences (default 90)

Parameters to tune ChimeraMaligner:

Scoring parameters:
-M
match score (default: +5)
-N
mismatch penalty (default: -4)
-Q
min query coverage by matching database sequence (default: 70)
-T
maximum traverses of the multiple alignment (default: 1)

Flags:

--printAlignments
(default off)
-v
verbose
--exec_dir
cd here before running

SEE ALSO

http://microbiomeutil.sourceforge.net/

AUTHOR

This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other distribution.
June 2013 cm_to_wigeon