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]
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[-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]
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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>
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2) With reference but without genbank file: python Parsnp.py -r <reference_genome> -d <seq_file1 seq_file2 ...> -p <threads>
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3) Autorecruit reference to a draft assembly: python Parsnp.py -q <draft_assembly> -d <seq_file1 seq_file2 ...> -p <threads>
optional arguments:
- -h, --help
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show this help message and exit
Input/Output:
- -c, --curated
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(c)urated genome directory, use all genomes in dir and ignore MUMi?
- -d SEQUENCES [SEQUENCES ...], --sequences SEQUENCES [SEQUENCES ...]
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A list of files containing genomes/contigs/scaffolds
- -r REFERENCE, --reference REFERENCE
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(r)eference genome (set to ! to pick random one from sequence dir)
- -g GENBANK [GENBANK ...], --genbank GENBANK [GENBANK ...]
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A list of Genbank file(s) (gbk)
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
- -q QUERY, --query QUERY
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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
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Max MUMi distance value for MUMi distribution
- -mmd MAX_MUMI_DISTANCE, --max-mumi-distance MAX_MUMI_DISTANCE
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Max MUMi distance (default: autocutoff based on distribution of MUMi values)
- -F, --fastmum
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Fast MUMi calculation
- -M, --mumi_only, --onlymumi
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Calculate MUMi and exit? overrides all other choices!
- --use-ani
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Use ani for genome recruitment
- --min-ani MIN_ANI
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Min ANI value to allow for genome recruitment.
- --use-mash
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Use mash for genome recruitment
- --max-mash-dist MAX_MASH_DIST
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Max mash distance.
MUM search:
- -a MIN_ANCHOR_LENGTH, --min-anchor-length MIN_ANCHOR_LENGTH, --anchorlength MIN_ANCHOR_LENGTH
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Min (a)NCHOR length (default = 1.1*(Log(S)))
- -m MUM_LENGTH, --mum-length MUM_LENGTH, --mumlength MUM_LENGTH
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Mum length
- -C MAX_CLUSTER_D, --max-cluster-d MAX_CLUSTER_D, --clusterD MAX_CLUSTER_D
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Maximal cluster D value
- -z MIN_CLUSTER_SIZE, --min-cluster-size MIN_CLUSTER_SIZE, --minclustersize MIN_CLUSTER_SIZE
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Minimum cluster size
LCB alignment:
- -D MAX_DIAG_DIFF, --max-diagonal-difference MAX_DIAG_DIFF, --DiagonalDiff MAX_DIAG_DIFF
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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}
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Alignment program to use
- -u, --unaligned
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Output unaligned regions
LCB Extensions:
- --extend-lcbs
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Extend the boundaries of LCBs with an ungapped alignment
- --match-score MATCH_SCORE
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Value of match score for extension
- --mismatch-penalty MISMATCH_PENALTY
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Value of mismatch score for extension (should be negative)
- --gap-penalty GAP_PENALTY
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Value of gap penalty for extension (should be negative)
Misc:
- --skip-phylogeny
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Do not generate phylogeny from core SNPs
- --validate-input
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Use Biopython to validate input files
- --use-fasttree
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Use fasttree instead of RaxML
- --vcf
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Generate VCF file.
- -p THREADS, --threads THREADS
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Number of threads to use
- -P MAX_PARTITION_SIZE, --max-partition-size MAX_PARTITION_SIZE
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Max partition size (limits memory usage)
- -v, --verbose
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Verbose output
-x, --xtrafast
-i INIFILE, --inifile INIFILE, --ini-file INIFILE
-e, --extend
- -V, --version
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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.