NAME

       parsnp - rapid core genome multi-alignment

SYNOPSIS

       parsnp [options] [-g|-r|-q] -d <genome_dir> -p <threads>

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.

OPTIONS

   input/output
       -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)

       -d = <path>: (d)irectory containing genomes/contigs/scaffolds

       -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)

       -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)

       -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]

       -q  =  <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome
              dir (default = NONE)

   MUMi
       -U = <float>: max MUMi distance value for MUMi distribution

       -M = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)

       -i = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)

   MUM search
       -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))

       -C = <int>: maximal cluster D value? (default=100)

       -z = <path>: min LCB si(z)e? (default = 25)

   LCB alignment
       -D = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp  (e.g.  100bp)  (default  =
              0.12)

       -e = <flag> greedily extend LCBs? experimental! (default = NO)

       -n = <string>: alignment program (default: libMUSCLE)

       -u = <flag>: output unaligned regions? .unaligned (default: NO)

   Recombination filtration
       -x  =  <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default:
              NO)

   Misc
       -h = <flag>: (h)elp: print this message and exit

       -p = <int>: number of threads to use? (default= 1)

       -P = <int>: max partition size? limits memory usage (default= 15000000)

       -v = <flag>: (v)erbose output? (default = NO)

       -V = <flag>: output (V)ersion and exit

EXAMPLES

       Parsnp quick start for three example scenarios:

   With reference & genbank file:
              parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads>

   With reference but without genbank file:
              parsnp -r <reference_genome> -d <genome_dir> -p <threads>

   Autorecruit reference to a draft assembly:
              parsnp -q <draft_assembly> -d <genome_db> -p <threads>

SEE ALSO

       For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.