.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.