[med-svn] r13831 - trunk/packages/microbiomeutil/trunk/debian

Tue Jun 4 14:34:57 UTC 2013

Author: tille
Date: 2013-06-04 14:34:57 +0000 (Tue, 04 Jun 2013)
New Revision: 13831

Added:
   trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.1
   trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.manpages
   trunk/packages/microbiomeutil/trunk/debian/nast-ier.1
   trunk/packages/microbiomeutil/trunk/debian/nast-ier.manpages
Modified:
   trunk/packages/microbiomeutil/trunk/debian/changelog
   trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links
Log:
Add nast-ier.1 (and commit chimeraslayer.1)


Modified: trunk/packages/microbiomeutil/trunk/debian/changelog
===================================================================

--- trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-04 14:32:53 UTC (rev 13830)
+++ trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-04 14:34:57 UTC (rev 13831)
@@ -19,7 +19,7 @@
     file with citation information
   * Removed debian/{ChimeraSlayer,microbiomeutil.install} because
     unneeded
-  * debian/chimeraslayer.1: Wrote manpage
+  * debian/*.1: Wrote manpages
   * debian/microbiomeutil.links: Synonyms with camel case spelling
     as in the provided documentation
   * debian/patches/hardening.patch: Enable propagation of hardening options

Added: trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.1
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.1	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.1	2013-06-04 14:34:57 UTC (rev 13831)
@@ -0,0 +1,88 @@
+.TH CHIMERASLAYER "1" "June 2013" "chimeraslayer " "User Commands"
+.SH NAME
+chimeraslayer \- detects likely chimeras in PCR amplified DNA
+.SH DESCRIPTION
+ChimeraSlayer is a chimeric sequence detection utility, compatible with
+near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
+.PP
+Chimera Slayer involves the following series of steps that operate to
+flag chimeric 16S rRNA sequences:
+.IP 1.
+the ends of a query sequence are searched against an included
+database of reference chimera-free 16S sequences to identify potential
+parents of a chimera
+.IP 2.
+candidate parents of a chimera are selected as those that form a
+branched best scoring alignment to the NAST-formatted query sequence
+.IP 3.
+the NAST alignment of the query sequence is improved in a
+‘chimera-aware’ profile-based NAST realignment to the selected
+reference parent sequences
+.IP 4.
+an evolutionary framework is used to flag query sequences found to
+exhibit greater sequence homology to an in silico chimera formed
+between any two of the selected reference parent sequences.
+.PP
+To run Chimera Slayer, you need NAST-formatted sequences generated by
+the nast-ier utility.
+.PP
+ChimeraSlayer is part of the microbiomeutil suite.
+
+.SH OPTIONS
+.SS Required
+.IP \fB\-\-query_NAST\fR
+multi\-fasta file containing query sequences in alignment format
+.PP
+.SS Common options
+.IP \fB\-\-db_NAST\fR
+db in NAST format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta\fP)
+.IP \fB\-\-db_FASTA\fR
+db in fasta format (megablast formatted) (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.fasta\fP)
+.IP \fB\-n\fR
+number of top matching database sequences to compare to (default 15)
+.IP \fB\-R\fR
+min divergence ratio default: 1.007
+.IP \fB\-P\fR
+min percent identity among matching sequences (default: 90)
+.SS Parameters to tune ChimeraParentSelector:
+Scoring parameters:
+.IP \fB\-M\fR
+match score   (default: +5)
+.IP \fB\-N\fR
+mismatch penalty  (default: \fB\-4\fR)
+.IP \fB\-Q\fR
+min query coverage by matching database sequence (default: 70)
+.IP \fB\-T\fR
+maximum traverses of the multiple alignment  (default: 1)
+.SS Parameters to tune ChimeraPhyloChecker
+.IP \fB\-\-windowSize\fR
+default 50
+.IP \fB\-\-windowStep\fR
+default 5
+.IP \fB\-\-minBS\fR
+minimum bootstrap support for calling chimera (default: 90)
+.IP \fB\-\-num_BS_replicates\fR
+default: 100
+.IP \fB\-\-low_range_finer_BS\fR
+(default: 10)
+If computed BS is between minBS and (minBS \- low_range_finer_BS), then num_finer_BS_replicates computed.
+.IP \fB\-\-num_finer_BS_replicates\fR
+(default: 1000)
+.IP \fB\-S\fR
+percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)
+.IP \fB\-\-num_parents_test\fR
+number of potential parents to test for chimeras (default: 3)
+.IP \fB\-\-MAX_CHIMERA_PARENT_PER_ID\fR
+Chimera/Parent alignments with perID above this are considered non\-chimeras (default 100; turned off)
+.SS Misc options
+.IP \fB\-\-printFinalAlignments\fR
+shows alignment between query sequence and pair of candidate chimera parents
+.IP \fB\-\-printCSalignments\fR
+print ChimeraSlayer alignments in ChimeraSlayer output
+.IP \fB\-\-exec_dir\fR
+chdir to here before running
+.SH "SEE ALSO"
+http://microbiomeutil.sourceforge.net/#A_CS
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.

Added: trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.manpages
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.manpages	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/chimeraslayer.manpages	2013-06-04 14:34:57 UTC (rev 13831)
@@ -0,0 +1 @@
+debian/chimeraslayer.1

Modified: trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links	2013-06-04 14:32:53 UTC (rev 13830)
+++ trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links	2013-06-04 14:34:57 UTC (rev 13831)
@@ -2,3 +2,4 @@
 usr/bin/nast-ier	usr/bin/NAST-iEr
 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

Added: trunk/packages/microbiomeutil/trunk/debian/nast-ier.1
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/nast-ier.1	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/nast-ier.1	2013-06-04 14:34:57 UTC (rev 13831)
@@ -0,0 +1,30 @@
+.TH NAST-IER "1" "June 2013" "nast-ier " "User Commands"
+.SH NAME
+nast-ier \- NAST-based DNA alignment tool
+.SH DESCRIPTION
+The NAST-iEr alignment utility aligns a single raw nucleotide sequence
+against one or more NAST formatted sequences.
+.PP
+The alignment algorithm involves global dynamic programming profile
+alignment to fixed (NAST-formatted) multiply aligned template sequences
+without any end-gap penalty.
+.PP
+NAST-iEr is part of the microbiomeutil suite.
+.SH OPTIONS
+.SS Required:
+.IP \fB\-\-query_FASTA\fR
+query database in FASTA format (seqs to NAST\-align)
+.SS Optional: (unless defaults are not set!)
+.IP \fB\-\-db_NAST\fR
+reference database in NAST format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta\fP)
+.IP \fB\-\-db_FASTA\fR
+reference database in FASTA format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.fasta\fP)
+.IP \fB\-\-num_top_hits\fR
+number of top hits to use for profile\-alignment (default: 10)
+.IP \fB\-\-Evalue\fR
+Evalue cutoff for top hits (default: 1e\-50)
+.SH "SEE ALSO"
+http://microbiomeutil.sourceforge.net/#A_NASTiEr
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.

Added: trunk/packages/microbiomeutil/trunk/debian/nast-ier.manpages
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/nast-ier.manpages	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/nast-ier.manpages	2013-06-04 14:34:57 UTC (rev 13831)
@@ -0,0 +1 @@
+debian/nast-ier.1


