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.