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

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>