parsnp1

Rapid core genome multi-alignment

Overview

|--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

Releases

5 releases since Debian 9 (Stretch); the text changed 1 time.

--DiagonalDiff since Debian 12 (Bookworm); --MUMi since Debian 12 (Bookworm); --alignment-program since Debian 12 (Bookworm); --alignmentprog since Debian 12 (Bookworm); --anchorlength since Debian 12 (Bookworm); --clusterD since Debian 12 (Bookworm); --curated since Debian 12 (Bookworm); --extend-lcbs since Debian 12 (Bookworm); --fastmum since Debian 12 (Bookworm); --gap-penalty since Debian 12 (Bookworm); --help since Debian 12 (Bookworm); --match-score since Debian 12 (Bookworm); --max-cluster-d since Debian 12 (Bookworm); --max-diagonal-difference since Debian 12 (Bookworm); --max-mash-dist since Debian 12 (Bookworm); --max-mumi-distance since Debian 12 (Bookworm); --max-mumi-distr-dist since Debian 12 (Bookworm); --max-partition-size since Debian 12 (Bookworm); --min-anchor-length since Debian 12 (Bookworm); --min-ani since Debian 12 (Bookworm); --min-cluster-size since Debian 12 (Bookworm); --minclustersize since Debian 12 (Bookworm); --mismatch-penalty since Debian 12 (Bookworm); --mum-length since Debian 12 (Bookworm); --mumi_only since Debian 12 (Bookworm); --mumlength since Debian 12 (Bookworm); --onlymumi since Debian 12 (Bookworm); --query since Debian 12 (Bookworm); --reference since Debian 12 (Bookworm); --skip-phylogeny since Debian 12 (Bookworm); --threads since Debian 12 (Bookworm); --unaligned since Debian 12 (Bookworm); --use-ani since Debian 12 (Bookworm); --use-fasttree since Debian 12 (Bookworm); --use-mash since Debian 12 (Bookworm); --validate-input since Debian 12 (Bookworm); --vcf since Debian 12 (Bookworm); --verbose since Debian 12 (Bookworm); --version since Debian 12 (Bookworm); -C since Debian 12 (Bookworm); -D since Debian 12 (Bookworm); -F since Debian 12 (Bookworm); -M since Debian 12 (Bookworm); -P since Debian 12 (Bookworm); -U since Debian 12 (Bookworm); -V since Debian 12 (Bookworm); -a since Debian 12 (Bookworm); -c since Debian 12 (Bookworm); -h since Debian 12 (Bookworm); -m since Debian 12 (Bookworm); -mmd since Debian 12 (Bookworm); -n since Debian 12 (Bookworm); -p since Debian 12 (Bookworm); -q since Debian 12 (Bookworm); -r since Debian 12 (Bookworm); -u since Debian 12 (Bookworm); -v since Debian 12 (Bookworm); -z since Debian 12 (Bookworm).