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.

parsnp 1.5.4                                       April 2022                                          PARSNP(1)