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PARSNP(1) User Commands PARSNP(1)


parsnp - rapid core genome multi-alignment


|--Parsnp 1.5.6--| For detailed documentation please see --> 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 -g <reference_genbank_file1 reference_genbank_file2 ...> -d <seq_file1 seq_file2 ...> -p <threads>
2) With reference but without genbank file: python -r <reference_genome> -d <seq_file1 seq_file2 ...> -p <threads>
3) Autorecruit reference to a draft assembly: python -q <draft_assembly> -d <seq_file1 seq_file2 ...> -p <threads>

optional arguments:

show this help message and exit


(c)urated genome directory, use all genomes in dir and ignore MUMi?
A list of files containing genomes/contigs/scaffolds
(r)eference genome (set to ! to pick random one from sequence dir)
A list of Genbank file(s) (gbk)

-o OUTPUT_DIR, --output-dir OUTPUT_DIR

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


Max MUMi distance value for MUMi distribution
Max MUMi distance (default: autocutoff based on distribution of MUMi values)
Fast MUMi calculation
Calculate MUMi and exit? overrides all other choices!
Use ani for genome recruitment
Min ANI value to allow for genome recruitment.
Use mash for genome recruitment
Max mash distance.

MUM search:

Min (a)NCHOR length (default = 1.1*(Log(S)))
Mum length
Maximal cluster D value
Minimum cluster size

LCB alignment:

Maximal diagonal difference. Either percentage (e.g. 0.2) or bp (e.g. 100bp)
Alignment program to use
Output unaligned regions

LCB Extensions:

Extend the boundaries of LCBs with an ungapped alignment
Value of match score for extension
Value of mismatch score for extension (should be negative)
Value of gap penalty for extension (should be negative)


Do not generate phylogeny from core SNPs
Use Biopython to validate input files
Use fasttree instead of RaxML
Generate VCF file.
Number of threads to use
Max partition size (limits memory usage)
Verbose output

-x, --xtrafast

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

-e, --extend

show program's version number and exit


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

April 2022 parsnp 1.5.4