PILERCR(1)

💖 PILERCR(1) 💖

okay bestie, you've found the manual page for pilercr, a User Command, and honestly? she's iconic. let's get into it.

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✨ NAME ✨

pilercr — software for finding CRISPR repeats 🧬✨

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🦋 DESCRIPTION 🦋

so like, the whole vibe here is:

pilercr v1.06 http://www.drive5.com/piler

that's it, that's the description. short. mysterious. main character energy. 💅

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👑 AUTHOR 👑

Written by Robert C. Edgar. This software is donated to the public domain. Please visit web site for requested citation. (yes bestie, cite her, she deserves it 🫶)

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🌸 Basic options 🌸

these are the starter pack, the bare minimum, the getting-ready-with-me of options:

• -in <filename> — the sequence file you wanna analyze (FASTA format). this is literally the whole point.
• -out <filename> — name of the report file (plain text). where the receipts go 📝
• -seq <filename> — save consensus sequences to this FASTA file.
• -trimseqs — eliminate similar seqs from the -seq file. decluttering, we love to see it ✨
• -noinfo — don't write help to report file. no extra yapping.
• -quiet — don't write progress messages to stderr. she's silent, she's mysterious, she's working 🔇

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🎀 Criteria for CRISPR detection, defaults in parentheses 🎀

this is the vibe check section. all the thresholds. all the defaults are sitting right there in the parentheses so you don't have to guess, periodt.

• -minarray <N> — must be at least <n> repeats in array (3).
• -mincons <F> — minimum conservation (0.9). At least N repeats must have identity >= F with the consensus sequence. Value is in range 0 .. 1.0. It is recommended to use a value < 1.0 because using 1.0 may suppress true arrays due to boundary misidentification.

⚠️ okay so this is a real one bestie: don't set it to 1.0. like, the manpage itself said it's not recommended. 1.0 is giving "too strict" and it'll ghost your actual arrays. 😭

• -minrepeat <L> — minimum repeat length (16).
• -maxrepeat <L> — maximum repeat length (64).
• -minspacer <L> — minimum spacer length (8).
• -maxspacer <L> — maximum spacer length (64).
• -minrepeatratio <R> — minimum repeat ratio (0.9).
• -minspacerratio <R> — minimum spacer ratio (0.75). 'Ratios' are defined as minlength / maxlength, thus a value close to 1.0 requires lengths to be similar, 1.0 means identical lengths. Spacer lengths sometimes vary significantly, so the default ratio is smaller. As with -mincons, using 1.0 is not recommended.

🙈 yeah so same warning energy as -mincons — 1.0 is not it. spacers be doing their own thing sometimes, so the default ratio is lower on purpose. lowkey genius, honestly.

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🧚 Parameters for creating local alignments 🧚

the fine-tuning era. getting into the details, as she should 💜

• -minhitlength <L> — minimum alignment length (16).
• -minid <F> — minimum identity (0.94).

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and that's the whole page, bestie. slay. 💅✨

pilercr 1.06+dfsg 🌈 August 2021 🎀 — that's the version and date, mwah, go forth and find those repeats 🦋💖