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commit 5fb2bfa755d56162056fc94d5617d263a3602678 Author: Andreas Tille <[email protected]> Date: Thu Jul 21 09:14:37 2016 +0200 Add manpage --- debian/manpages | 1 + debian/parsnp.1 | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 diff --git a/debian/parsnp.1 b/debian/parsnp.1 new file mode 100644 index 0000000..0c5a0f6 --- /dev/null +++ b/debian/parsnp.1 @@ -0,0 +1,80 @@ +.TH PARSNP "1" "July 2016" "parsnp 1.2" "User Commands" +.SH NAME +parsnp \- rapid core genome multi-alignment +.SH SYNOPSIS +.B parsnp +[options] [\-g|\-r|\-q] \fB\-d\fR <genome_dir> \fB\-p\fR <threads> +.SH DESCRIPTION +Parsnp was designed to align the core genome of hundreds to thousands of +bacterial genomes within a few minutes to few hours. Input can be both +draft assemblies and finished genomes, and output includes variant (SNP) +calls, core genome phylogeny and multi-alignments. Parsnp leverages +contextual information provided by multi-alignments surrounding SNP +sites for filtration/cleaning, in addition to existing tools for +recombination detection/filtration and phylogenetic reconstruction. +.SH OPTIONS +.SS input/output +.HP +\fB\-c\fR = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO) +.HP +\fB\-d\fR = <path>: (d)irectory containing genomes/contigs/scaffolds +.HP +\fB\-r\fR = <path>: (r)eference genome (set to ! to pick random one from genome dir) +.HP +\fB\-g\fR = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None) +.HP +\fB\-o\fR = <string>: output directory? default [./P_CURRDATE_CURRTIME] +.HP +\fB\-q\fR = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE) +.SS MUMi +.HP +\fB\-U\fR = <float>: max MUMi distance value for MUMi distribution +.HP +\fB\-M\fR = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO) +.HP +\fB\-i\fR = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values) +.SS MUM search +.HP +\fB\-a\fR = <int>: min (a)NCHOR length (default = 1.1*Log(S)) +.HP +\fB\-C\fR = <int>: maximal cluster D value? (default=100) +.HP +\fB\-z\fR = <path>: min LCB si(z)e? (default = 25) +.SS LCB alignment +.HP +\fB\-D\fR = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12) +.HP +\fB\-e\fR = <flag> greedily extend LCBs? experimental! (default = NO) +.HP +\fB\-n\fR = <string>: alignment program (default: libMUSCLE) +.HP +\fB\-u\fR = <flag>: output unaligned regions? .unaligned (default: NO) +.SS Recombination filtration +.HP +\fB\-x\fR = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO) +.SS Misc +.HP +\fB\-h\fR = <flag>: (h)elp: print this message and exit +.HP +\fB\-p\fR = <int>: number of threads to use? (default= 1) +.HP +\fB\-P\fR = <int>: max partition size? limits memory usage (default= 15000000) +.HP +\fB\-v\fR = <flag>: (v)erbose output? (default = NO) +.HP +\fB\-V\fR = <flag>: output (V)ersion and exit +.SH EXAMPLES +Parsnp quick start for three example scenarios: +.SS With reference & genbank file: +.IP +parsnp \fB\-g\fR <reference_genbank_file1,reference_genbank_file2,..> \fB\-d\fR <genome_dir> \fB\-p\fR <threads> +.SS With reference but without genbank file: +.IP +parsnp \fB\-r\fR <reference_genome> \fB\-d\fR <genome_dir> \fB\-p\fR <threads> +.SS Autorecruit reference to a draft assembly: +.IP +parsnp \fB\-q\fR <draft_assembly> \fB\-d\fR <genome_db> \fB\-p\fR <threads> +.SH SEE ALSO +For detailed documentation please see \fB\-\-\fR> http://harvest.readthedocs.org/en/latest +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/parsnp.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
