MASH-TRIANGLE(1)

💖 MASH-TRIANGLE(1) 💖

okay bestie, welcome to the mash-triangle manual page, straight out of section 1 of the manual, and no cap it's a good one 🦋

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✨ NAME ✨

mash-triangle — estimate a lower-triangular distance matrix 👑

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🌸 SYNOPSIS 🌸

mash triangle [options] <seq1> [<seq2>] ...

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🎀 DESCRIPTION 🎀

So what this does, bestie, is it estimates the distance of each input sequence to every other input sequence. The way it gives it to you is a lower-triangular distance matrix, written out in relaxed Phylip format 💅

Your input sequences can be literally any of these:

• fasta
• fastq
• gzipped or not (either one, we don't judge) 🫶
• Mash sketch files (.msh) — but only ones with matching k-mer sizes, okay? mismatched k-mer sizes is not the vibe.

Input files can also be files of file names — peep -l for that one 👀

And if you hand it more than one input file, then by default it compares whole files against each other. Want it to compare individual sequences instead? That's -i. iykyk ✨

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💅 OPTIONS 💅

• -h — Help. the classic. ask and ye shall receive 🙈
• -p <int> — Parallelism, bestie. This many threads will be spawned for processing. Default is [1]. go on, give it more, she can handle it 🔥

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🦋 Input 🦋

• -l — List input. Each query file contains a list of sequence files, one per line. The reference file is not affected by this. periodt.

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🌈 Output 🌈

• -C — Use comment fields for sequence names instead of IDs. cute names, no numbers 💖
• -E — Output an edge list instead of a Phylip matrix. The fields are [seq1, seq2, dist, p-val, shared-hashes]. iconic format honestly ✨
• -v <num> — Maximum p-value to report in the edge list. Implies -E. Range is (0-1), default [1.0].
• -d <num> — Maximum distance to report in the edge list. Implies -E. Range is (0-1), default [1.0].

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🧚 Sketching 🧚

• -k <int> — K-mer size, babes. Hashes will be based on strings of this many nucleotides. Canonical nucleotides are used by default — go look at the Alphabet options below for the tea. Range is (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. This is the one you want for multi-fastas of single-chromosome genomes, or for pair-wise gene comparisons. so specific, so useful 💜
• -w <num> — Probability threshold for warning about low k-mer size. Range (0-1), default [0.01] 👀
• -r — Input is a read set. Go check the Reads options below. Incompatible with -i — pick a lane bestie, you cannot have both 🚫

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🍓 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. Super useful if exact filtering with -m is eating too much memory. But heads up: some unique k-mers may pass erroneously, and copies cannot be counted beyond 2. Implies -r. ⚠️
• -m <int> — Minimum copies of each k-mer required to pass the 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 you specify it, it'll be used for p-value calculation instead of an estimated size from k-mer content. Implies -r. 🌸

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💜 Sketching (alphabet) 💜

• -n — Preserve strand. By default, strand is ignored by using canonical DNA k-mers, which are the alphabetical minima of forward-reverse pairs. Implied if an alphabet is specified with -a or -z. 🧬
• -a — Use the 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) — go read that one too, bestie, they're a set 🫶

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and that's the whole page!! go forth and triangle your distances, you absolute main character 💅✨

this page is from the MASH-TRIANGLE(1) manual, dated 2019-12-13 — yeah she's an oldie but a goodie, still slaying after all this time 👑💖