---
name: "parsnp"
section: "1"
platform: "linux"
package: "parsnp"
version: "2.1.3+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/parsnp"
---

# parsnp(1)

rapid core genome multi-alignment

## NAME

parsnp - rapid core genome multi-alignment

## DESCRIPTION

\|--Parsnp 1.5.6--\| For detailed documentation please see **--**\> http://harvest.readthedocs.org/en/latest usage: parsnp \[-h\] \[-c\] **-d** SEQUENCES \[SEQUENCES ...\] \[-r REFERENCE\]

-

  \[-g GENBANK \[GENBANK ...\]\] \[-o OUTPUT\_DIR\] \[-q QUERY\] \[-U MAX\_MUMI\_DISTR\_DIST \| **-mmd** MAX\_MUMI\_DISTANCE\] \[-F\] \[-M\] \[--use-ani\] \[--min-ani MIN\_ANI\] \[--use-mash\] \[--max-mash-dist MAX\_MASH\_DIST\] \[-a MIN\_ANCHOR\_LENGTH\] \[-m MUM\_LENGTH\] \[-C MAX\_CLUSTER\_D\] \[-z MIN\_CLUSTER\_SIZE\] \[-D MAX\_DIAG\_DIFF\] \[-n {mafft,muscle,fsa,prank}\] \[-u\] \[--use-fasttree\] \[--vcf\] \[-p THREADS\] \[-P MAX\_PARTITION\_SIZE\] \[-v\] \[-x\] \[-i INIFILE\] \[-e\] \[-V\]

-

  Parsnp quick start for three example scenarios: 1) With reference & genbank file: python Parsnp.py **-g** \<reference\_genbank\_file1 reference\_genbank\_file2 ...\> **-d** \<seq\_file1 seq\_file2 ...\>  **-p** \<threads\>

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  2\) With reference but without genbank file: python Parsnp.py **-r** \<reference\_genome\> **-d** \<seq\_file1 seq\_file2 ...\> **-p** \<threads\>

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  3\) Autorecruit reference to a draft assembly: python Parsnp.py **-q** \<draft\_assembly\> **-d** \<seq\_file1 seq\_file2 ...\> **-p** \<threads\>

### optional arguments:

- **-h**, **--help**

  show this help message and exit

### Input/Output:

- **-c**, **--curated**

  (c)urated genome directory, use all genomes in dir and ignore MUMi?

- **-d** SEQUENCES \[SEQUENCES ...\], **--sequences** SEQUENCES \[SEQUENCES ...\]

  A list of files containing genomes/contigs/scaffolds

- **-r** REFERENCE, **--reference** REFERENCE

  (r)eference genome (set to ! to pick random one from sequence dir)

- **-g** GENBANK \[GENBANK ...\], **--genbank** GENBANK \[GENBANK ...\]

  A list of Genbank file(s) (gbk)

**-o** OUTPUT\_DIR, **--output-dir** OUTPUT\_DIR

- **-q** QUERY, **--query** QUERY

  Specify (assembled) query genome to use, in addition to genomes found in genome dir

### MUMi:

- **-U** MAX\_MUMI\_DISTR\_DIST, **--max-mumi-distr-dist** MAX\_MUMI\_DISTR\_DIST, **--MUMi** MAX\_MUMI\_DISTR\_DIST

  Max MUMi distance value for MUMi distribution

- **-mmd** MAX\_MUMI\_DISTANCE, **--max-mumi-distance** MAX\_MUMI\_DISTANCE

  Max MUMi distance (default: autocutoff based on distribution of MUMi values)

- **-F**, **--fastmum**

  Fast MUMi calculation

- **-M**, **--mumi\_only**, **--onlymumi**

  Calculate MUMi and exit? overrides all other choices!

- **--use-ani**

  Use ani for genome recruitment

- **--min-ani** MIN\_ANI

  Min ANI value to allow for genome recruitment.

- **--use-mash**

  Use mash for genome recruitment

- **--max-mash-dist** MAX\_MASH\_DIST

  Max mash distance.

### MUM search:

- **-a** MIN\_ANCHOR\_LENGTH, **--min-anchor-length** MIN\_ANCHOR\_LENGTH, **--anchorlength** MIN\_ANCHOR\_LENGTH

  Min (a)NCHOR length (default = 1.1\*(Log(S)))

- **-m** MUM\_LENGTH, **--mum-length** MUM\_LENGTH, **--mumlength** MUM\_LENGTH

  Mum length

- **-C** MAX\_CLUSTER\_D, **--max-cluster-d** MAX\_CLUSTER\_D, **--clusterD** MAX\_CLUSTER\_D

  Maximal cluster D value

- **-z** MIN\_CLUSTER\_SIZE, **--min-cluster-size** MIN\_CLUSTER\_SIZE, **--minclustersize** MIN\_CLUSTER\_SIZE

  Minimum cluster size

### LCB alignment:

- **-D** MAX\_DIAG\_DIFF, **--max-diagonal-difference** MAX\_DIAG\_DIFF, **--DiagonalDiff** MAX\_DIAG\_DIFF

  Maximal diagonal difference. Either percentage (e.g. 0.2) or bp (e.g. 100bp)

- **-n** {mafft,muscle,fsa,prank}, **--alignment-program** {mafft,muscle,fsa,prank}, **--alignmentprog** {mafft,muscle,fsa,prank}

  Alignment program to use

- **-u**, **--unaligned**

  Output unaligned regions

### LCB Extensions:

- **--extend-lcbs**

  Extend the boundaries of LCBs with an ungapped alignment

- **--match-score** MATCH\_SCORE

  Value of match score for extension

- **--mismatch-penalty MISMATCH\_PENALTY**

  **Value of mismatch score for extension (should be negative)**

- **--gap-penalty GAP\_PENALTY**

  **Value of gap penalty for extension (should be negative)**

### Misc:

- **--skip-phylogeny**

  Do not generate phylogeny from core SNPs

- **--validate-input**

  Use Biopython to validate input files

- **--use-fasttree**

  Use fasttree instead of RaxML

- **--vcf**

  Generate VCF file.

- **-p** THREADS, **--threads** THREADS

  Number of threads to use

- **-P** MAX\_PARTITION\_SIZE, **--max-partition-size** MAX\_PARTITION\_SIZE

  Max partition size (limits memory usage)

- **-v**, **--verbose**

  Verbose output

**-x**, **--xtrafast**

**-i** INIFILE, **--inifile** INIFILE, **--ini-file** INIFILE

**-e**, **--extend**

- **-V**, **--version**

  show program's version number and exit

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.