.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PARSNP "1" "April 2022" "parsnp 1.5.4" "User Commands"
.SH NAME
parsnp \- rapid core genome multi-alignment
.SH DESCRIPTION
|\-\-Parsnp 1.5.6\-\-|
For detailed documentation please see \fB\-\-\fR> http://harvest.readthedocs.org/en/latest
usage: parsnp [\-h] [\-c] \fB\-d\fR SEQUENCES [SEQUENCES ...] [\-r REFERENCE]
.IP
[\-g GENBANK [GENBANK ...]] [\-o OUTPUT_DIR] [\-q QUERY]
[\-U MAX_MUMI_DISTR_DIST | \fB\-mmd\fR 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]
.IP
Parsnp quick start for three example scenarios:
1) With reference & genbank file:
python Parsnp.py \fB\-g\fR <reference_genbank_file1 reference_genbank_file2 ...> \fB\-d\fR <seq_file1 seq_file2 ...>  \fB\-p\fR <threads>
.IP
2) With reference but without genbank file:
python Parsnp.py \fB\-r\fR <reference_genome> \fB\-d\fR <seq_file1 seq_file2 ...> \fB\-p\fR <threads>
.IP
3) Autorecruit reference to a draft assembly:
python Parsnp.py \fB\-q\fR <draft_assembly> \fB\-d\fR <seq_file1 seq_file2 ...> \fB\-p\fR <threads>
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "Input/Output:"
.TP
\fB\-c\fR, \fB\-\-curated\fR
(c)urated genome directory, use all genomes in dir and ignore MUMi?
.TP
\fB\-d\fR SEQUENCES [SEQUENCES ...], \fB\-\-sequences\fR SEQUENCES [SEQUENCES ...]
A list of files containing genomes/contigs/scaffolds
.TP
\fB\-r\fR REFERENCE, \fB\-\-reference\fR REFERENCE
(r)eference genome (set to ! to pick random one from sequence dir)
.TP
\fB\-g\fR GENBANK [GENBANK ...], \fB\-\-genbank\fR GENBANK [GENBANK ...]
A list of Genbank file(s) (gbk)
.HP
\fB\-o\fR OUTPUT_DIR, \fB\-\-output\-dir\fR OUTPUT_DIR
.TP
\fB\-q\fR QUERY, \fB\-\-query\fR QUERY
Specify (assembled) query genome to use, in addition to genomes found in genome dir
.SS "MUMi:"
.TP
\fB\-U\fR MAX_MUMI_DISTR_DIST, \fB\-\-max\-mumi\-distr\-dist\fR MAX_MUMI_DISTR_DIST, \fB\-\-MUMi\fR MAX_MUMI_DISTR_DIST
Max MUMi distance value for MUMi distribution
.TP
\fB\-mmd\fR MAX_MUMI_DISTANCE, \fB\-\-max\-mumi\-distance\fR MAX_MUMI_DISTANCE
Max MUMi distance (default: autocutoff based on distribution of MUMi values)
.TP
\fB\-F\fR, \fB\-\-fastmum\fR
Fast MUMi calculation
.TP
\fB\-M\fR, \fB\-\-mumi_only\fR, \fB\-\-onlymumi\fR
Calculate MUMi and exit? overrides all other choices!
.TP
\fB\-\-use\-ani\fR
Use ani for genome recruitment
.TP
\fB\-\-min\-ani\fR MIN_ANI
Min ANI value to allow for genome recruitment.
.TP
\fB\-\-use\-mash\fR
Use mash for genome recruitment
.TP
\fB\-\-max\-mash\-dist\fR MAX_MASH_DIST
Max mash distance.
.SS "MUM search:"
.TP
\fB\-a\fR MIN_ANCHOR_LENGTH, \fB\-\-min\-anchor\-length\fR MIN_ANCHOR_LENGTH, \fB\-\-anchorlength\fR MIN_ANCHOR_LENGTH
Min (a)NCHOR length (default = 1.1*(Log(S)))
.TP
\fB\-m\fR MUM_LENGTH, \fB\-\-mum\-length\fR MUM_LENGTH, \fB\-\-mumlength\fR MUM_LENGTH
Mum length
.TP
\fB\-C\fR MAX_CLUSTER_D, \fB\-\-max\-cluster\-d\fR MAX_CLUSTER_D, \fB\-\-clusterD\fR MAX_CLUSTER_D
Maximal cluster D value
.TP
\fB\-z\fR MIN_CLUSTER_SIZE, \fB\-\-min\-cluster\-size\fR MIN_CLUSTER_SIZE, \fB\-\-minclustersize\fR MIN_CLUSTER_SIZE
Minimum cluster size
.SS "LCB alignment:"
.TP
\fB\-D\fR MAX_DIAG_DIFF, \fB\-\-max\-diagonal\-difference\fR MAX_DIAG_DIFF, \fB\-\-DiagonalDiff\fR MAX_DIAG_DIFF
Maximal diagonal difference. Either percentage (e.g. 0.2) or bp (e.g. 100bp)
.TP
\fB\-n\fR {mafft,muscle,fsa,prank}, \fB\-\-alignment\-program\fR {mafft,muscle,fsa,prank}, \fB\-\-alignmentprog\fR {mafft,muscle,fsa,prank}
Alignment program to use
.TP
\fB\-u\fR, \fB\-\-unaligned\fR
Output unaligned regions
.SS "LCB Extensions:"
.TP
\fB\-\-extend\-lcbs\fR
Extend the boundaries of LCBs with an ungapped alignment
.TP
\fB\-\-match\-score\fR MATCH_SCORE
Value of match score for extension
.TP
\fB\-\-mismatch\-penalty MISMATCH_PENALTY
Value of mismatch score for extension (should be negative)
.TP
\fB\-\-gap\-penalty GAP_PENALTY
Value of gap penalty for extension (should be negative)
.SS "Misc:"
.TP
\fB\-\-skip\-phylogeny\fR
Do not generate phylogeny from core SNPs
.TP
\fB\-\-validate\-input\fR
Use Biopython to validate input files
.TP
\fB\-\-use\-fasttree\fR
Use fasttree instead of RaxML
.TP
\fB\-\-vcf\fR
Generate VCF file.
.TP
\fB\-p\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads to use
.TP
\fB\-P\fR MAX_PARTITION_SIZE, \fB\-\-max\-partition\-size\fR MAX_PARTITION_SIZE
Max partition size (limits memory usage)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Verbose output
.HP
\fB\-x\fR, \fB\-\-xtrafast\fR
.HP
\fB\-i\fR INIFILE, \fB\-\-inifile\fR INIFILE, \fB\-\-ini\-file\fR INIFILE
.HP
\fB\-e\fR, \fB\-\-extend\fR
.TP
\fB\-V\fR, \fB\-\-version\fR
show program's version number and exit
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.