Man page - cm_to_wigeon(1)

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Package: wigeon
apt-get install wigeon

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wigeon

Manual

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

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