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Manual

PARSNP

NAME
DESCRIPTION
optional arguments:
Input/Output:
MUMi:
MUM search:
LCB alignment:
LCB Extensions:
Misc:
AUTHOR

---

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>

2) With reference but without genbank file: python Parsnp.py -r <reference_genome> -d <seq_file1 seq_file2 ...> -p <threads>

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.

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