Author: tille Date: 2013-06-04 15:00:12 +0000 (Tue, 04 Jun 2013) New Revision: 13832
Added: trunk/packages/microbiomeutil/trunk/debian/wigeon.1 trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages Modified: trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links Log: wigeon.1 Modified: trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links 2013-06-04 14:34:57 UTC (rev 13831) +++ trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links 2013-06-04 15:00:12 UTC (rev 13832) @@ -3,3 +3,4 @@ usr/bin/wigeon usr/bin/WigeoN usr/share/man/man1/chimeraslayer.1.gz usr/share/man/man1/ChimeraSlayer.1.gz usr/share/man/man1/nast-ier.1.gz usr/share/man/man1/NAST-iEr.1.gz +usr/share/man/man1/wigeon.1.gz usr/share/man/man1/WigeoN.1.gz Added: trunk/packages/microbiomeutil/trunk/debian/wigeon.1 =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/wigeon.1 (rev 0) +++ trunk/packages/microbiomeutil/trunk/debian/wigeon.1 2013-06-04 15:00:12 UTC (rev 13832) @@ -0,0 +1,44 @@ +.TH WIGEON "1" "June 2013" "wigeon " "User Commands" +.SH NAME +wigeon \- reimplementation of the Pintail 16S DNA anomaly detection utility +.SH 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. +.PP +WigeoN is a flexible command-line based reimplementation of the Pintail +algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36. +.PP +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. +.PP +To run WigeoN, you need NAST-formatted sequences generated by the +nast-ier utility. +.PP +WigeoN is part of the microbiomeutil suite. +.SH OPTIONS +.SS Required: +.IP \fB\-\-query_NAST\fR +multi\-fasta file containing query sequences in alignment format +.SS Optional: +.IP \fB\-\-db_NAST\fR +db in NAST format +.IP \fB\-\-db_FASTA\fR +db in fasta format (megablast formatted) +.IP \fB\-\-num_top_hits\fR +default 1: uses only the single best match. +.IP \fB\-\-plot\fR +.IP \fB\-\-DEBUG\fR +.IP \fB\-\-exec_dir\fR +cd to exec_dir before running +.PP +.SH "SEE ALSO" +http://microbiomeutil.sourceforge.net/#A_WigeoN +.SH AUTHOR +This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other +distribution. Added: trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages (rev 0) +++ trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages 2013-06-04 15:00:12 UTC (rev 13832) @@ -0,0 +1 @@ +debian/wigeon.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
