Download, install & run

Parsnp is distributed as a precompiled binary that should be devoid of external dependencies (all included in dist). The three steps below represent the fastest way to start using the software:


On Linux:

Basic usage:

From command-line:

parsnp –p <threads> –d <directory of genomes> –r <ref genome>

Advanced usage:

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>

Command-line parameters:


-c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)
-d = <path>: (d)irectory containing genomes/contigs/scaffolds
-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)
-r = <path>: (r)eference genome (set to ! to pick random one from genome dir)


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

SNP filters:

-R = <flag>: disable (R)epeat filtering?
-x = <flag>: enable recombination filtering? (default: NO)


-h = <flag>: (h)elp: print this message
-P = <int>: max partition size? limits memory usage (default= 15000000)
-p = <int>: number of threads to use? (default= 1)
-v = <flag>: (v)erbose output? (default = NO)

Output Files

  1. Newick formatted core genome SNP tree: $outputdir/parsnp.tree
  2. SNPs used to infer phylogeny: $outputdir/parsnp.vcf
  3. Gingr formatted binary archive: $outputdir/parsnp.ggr
  4. XMFA formatted multiple alignment: $outputdir/parsnp.xmfa