PARSNP(1)

🦋 NAME 🦋

okay bestie, gather round, it's parsnp — rapid core genome multi-alignment ✨ and yes, this is page one of the User Commands manual, section 1 energy only. 💅

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💖 DESCRIPTION 💖

first things first, the program screams its own name at you:

|--Parsnp 1.5.6--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

for detailed documentation please see that link up there, fr fr, go read it, it's giving thorough. 📚

then it drops the usage line on you like it's nothing:

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: 🎀 here are the three little starter packs, no cap:

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>

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✨ optional arguments ✨

• -h, --help — shows this help message and then dips. bye bestie 👋

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🗂️ Input/Output 🗂️

• -c, --curated — (c)urated genome directory moment: use all the genomes sitting in the dir, and ignore MUMi entirely. 💀
• -d SEQUENCES [SEQUENCES ...], --sequences SEQUENCES [SEQUENCES ...] — a whole list of files holding genomes/contigs/scaffolds. the main character input, lowkey.
• -r REFERENCE, --reference REFERENCE — the (r)eference genome. and get this: set it to ! and it'll just pick a random one from the sequence dir like it's pulling a card from a deck. 🎲
• -g GENBANK [GENBANK ...], --genbank GENBANK [GENBANK ...] — a list of Genbank file(s) (that's gbk to its friends).
• -o OUTPUT_DIR, --output-dir OUTPUT_DIR — no description in the original, bestie, it's mysterious like that 🫣
• -q QUERY, --query QUERY — specify an (assembled) query genome to use, on top of the genomes already chilling in the genome dir. extra credit behaviour.

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🧬 MUMi 🧬

• -U MAX_MUMI_DISTR_DIST, --max-mumi-distr-dist MAX_MUMI_DISTR_DIST, --MUMi MAX_MUMI_DISTR_DIST — max MUMi distance value for the MUMi distribution.
• -mmd MAX_MUMI_DISTANCE, --max-mumi-distance MAX_MUMI_DISTANCE — max MUMi distance. and the default? autocutoff based on the distribution of MUMi values, she picks for herself, iconic. 💅
• -F, --fastmum — fast MUMi calculation. zoom zoom. 🔥
• -M, --mumi_only, --onlymumi — calculate MUMi and then EXIT. and it overrides all other choices! like, all of them. every single one. 😭
• --use-ani — use ANI for genome recruitment.
• --min-ani MIN_ANI — min ANI value to allow for genome recruitment. the cutoff queen.
• --use-mash — use mash for genome recruitment.
• --max-mash-dist MAX_MASH_DIST — max mash distance.

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🔍 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)). math ate, honestly.
• -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.

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🧩 LCB alignment 🧩

• -D MAX_DIAG_DIFF, --max-diagonal-difference MAX_DIAG_DIFF, --DiagonalDiff MAX_DIAG_DIFF — maximal diagonal difference. you can give it either a percentage (like 0.2) or bp (like 100bp). flexible fr fr. 🌈
• -n {mafft,muscle,fsa,prank}, --alignment-program {mafft,muscle,fsa,prank}, --alignmentprog {mafft,muscle,fsa,prank} — which alignment program to use. pick your fighter: mafft, muscle, fsa, or prank. 👑
• -u, --unaligned — output unaligned regions.

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🌱 LCB Extensions 🌱

• --extend-lcbs — extends the boundaries of LCBs using an ungapped alignment. stretching that vibe. 🧘
• --match-score MATCH_SCORE — value of match score for the extension.
• --mismatch-penalty MISMATCH_PENALTY — value of mismatch score for the extension, and it should be negative, don't fight it.
• --gap-penalty GAP_PENALTY — value of gap penalty for the extension, also should be negative. yes, both of them. 😌

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🎀 Misc 🎀

• --skip-phylogeny — do NOT generate phylogeny from core SNPs. skipping, but make it fashion.
• --validate-input — use Biopython to validate the input files. safety first bestie. 🫶
• --use-fasttree — use fasttree instead of RaxML.
• --vcf — generate VCF file.
• -p THREADS, --threads THREADS — number of threads to use. feed her cores, she's hungry. 🔥
• -P MAX_PARTITION_SIZE, --max-partition-size MAX_PARTITION_SIZE — max partition size, which limits memory usage. very mindful, very demure.
• -v, --verbose — verbose output. she will tell you EVERYTHING. 🗣️
• -x, --xtrafast — the original literally says nothing else about this one 💀
• -i INIFILE, --inifile INIFILE, --ini-file INIFILE — also no description in the original, she's a mystery 🫣
• -e, --extend — same deal, no description given 😭
• -V, --version — shows the program's version number and then exits. slay and goodbye. ✨

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🌸 AUTHOR 🌸

this manpage was written by Nilesh Patra for the Debian distribution, and it can be used for any other usage of the program. credit given, credit due. 👑

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and that's a wrap, bestie 💖 this whole thing is parsnp 1.5.4, dated April 2022 — go align something gorgeous 🦋🌸