MASH-DIST(1)

💖 MASH-DIST(1) 💖

okay bestie, welcome to mash-dist — a little page from the MASH-DIST(1) manual, and honestly? it's giving distance-calculating icon. let's get into it 🦋

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✨ NAME ✨

mash-dist — estimate the distance of query sequences to references

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🌸 SYNOPSIS 🌸

mash dist [options] <reference> <query> [<query>] ...

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💅 DESCRIPTION 💅

So what we're doing here is estimating the distance of each query sequence to the reference. no cap, that's the whole job.

Both the reference and the queries can be:

• fasta or fastq
• gzipped or not gzipped
• Mash sketch files (.msh) — but only ones with matching k-mer sizes, okay? they gotta match. 👑

Query files can also be files of file names (peep -l for that one). And whole files are compared by default — if you'd rather do individual sequences, that's -i's whole thing.

The output fields, in order, are:

1. reference-ID
2. query-ID
3. distance
4. p-value
5. shared-hashes

periodt. 💫

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🎀 OPTIONS 🎀

• -h — Help. our fave, always there for u 🫶
• -p <int> — Parallelism. This many threads will be spawned for processing. default is [1].

🌈 Input

• -l — List input. Each query file contains a list of sequence files, one per line. The reference file is not affected. (the reference stays unbothered, as it should 💅)

⭐ Output

• -t — Table output. Heads up: it will not report p-values, but the fields will be blank if they do not meet the p-value threshold.
• -v <num> — Maximum p-value to report. range is (0-1), default [1.0].
• -d <num> — Maximum distance to report. range is (0-1), default [1.0].

🧚 Sketching

• -k <int> — K-mer size. Hashes will be based on strings of this many nucleotides. Canonical nucleotides are used by default (see the Alphabet options below 👀). range (1-32), default [21].
• -s <int> — Sketch size. Each sketch will have at most this many non-redundant min-hashes. default [1000].
• -i — Sketch individual sequences, rather than whole files.
• -w <num> — Probability threshold for warning about low k-mer size. range (0-1), default [0.01].
• -r — Input is a read set. See the Reads options below. Incompatible with -i. 🚫

🍓 Sketching (reads)

• -b <size> — Use a Bloom filter of this size (raw bytes or with K/M/G/T) to filter out unique k-mers. This is useful if exact filtering with -m uses too much memory. However, some unique k-mers may pass erroneously, and copies cannot be counted beyond 2. Implies -r.

lowkey important: that "some unique k-mers may pass erroneously" and "copies cannot be counted beyond 2" is real, bestie. not a drill. 😭

• -m <int> — Minimum copies of each k-mer required to pass noise filter for reads. Implies -r. default [1].
• -c <num> — Target coverage. Sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity). Implies -r.
• -g <size> — Genome size. If specified, will be used for p-value calculation instead of an estimated size from k-mer content. Implies -r.

💜 Sketching (alphabet)

• -n — Preserve strand (by default, strand is ignored by using canonical DNA k-mers, which are alphabetical minima of forward-reverse pairs). Implied if an alphabet is specified with -a or -z.
• -a — Use amino acid alphabet (A-Z, except BJOUXZ). Implies -n, -k 9.
• -z <text> — Alphabet to base hashes on (case ignored by default; see -Z). K-mers with other characters will be ignored. Implies -n.
• -Z — Preserve case in k-mers and alphabet (case is ignored by default). Sequence letters whose case is not in the current alphabet will be skipped when sketching.

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🔥 SEE ALSO 🔥

• mash(1)

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okay that's the whole page, you ate it, you're literally a mash dist expert now 💖 this lil manual page is from 2019-12-13, and it's the MASH-DIST(1) one — go forth and calculate those distances, bestie. slay 🎀✨