LASTDB(1)

📦 version 1654, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 LASTDB — ok bestie, let's build you a database 💖

So like. This is the lastdb manual page, and honestly? It's giving foundation. It's giving main character setup arc. Because lastdb is all about genome-scale comparison of biological sequences, and it's the thing you run before all the fun stuff happens. ✨

🌸 NAME 🌸

lastdb — genome-scale comparison of biological sequences 🧬

🦋 SYNOPSIS 🦋

lastdb [options] output-name fasta-sequence-file(s)

✨ DESCRIPTION ✨

Okay so here's the tea, bestie: lastdb prepares sequences for subsequent alignment with lastal. That's it. That's the whole job. You feed it your sequences, it does the prep work, and then lastal gets to shine. It's the backstage crew. The glam squad. The one who does your hair before the party. 💅

👑 OPTIONS 👑

🎀 Main Options 🎀

  • -h, --help — shows you all the options plus their default settings, then dips out (exits). Iconic behaviour, honestly.
  • -p — treats the sequences as proteins. Glow-up mode for amino acids.
  • -R — repeat-marking options (default=10). Yes, repeat. Like the group chat. 🔁
  • -c — soft-mask lowercase letters. lowercase = soft, uppercase = loud, we love a dress code.

🧚 Advanced Options (default settings) 🧚

These are the deep-lore settings. Defaults are in the parentheses, no cap.

  • -Q — input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (0)
  • -s — volume size (unlimited)
  • -m — seed pattern (non-DNA: 1)
  • -u — seeding scheme (DNA: YASS)
  • -w — index step (1)
  • -a — user-defined alphabet
  • -i — minimum limit on initial matches per query position (0)
  • -b — bucket depth
  • -C — child table type: 0=none, 1=byte-size, 2=short-size, 3=full (0)
  • -x — just count sequences and letters 🔢
  • -v — be verbose: write messages about what lastdb is doing. Basically it narrates its own life. Obsessed.
  • -V, --version — show version information, and exit
ngl bestie, -x and -v are the duo. One just counts, the other won't stop talking. Balance. ⚖️

😭 REPORTING BUGS 😭

Found a bug? Not the vibe, but okay, we fix it. 🫶

🌈 SEE ALSO 🌈

(nothing here in the original, but hi, hello, go run lastal next 💜)

And that's the whole page, bestie!! You now know lastdb top to bottom, every flag, every default, every value. No skipped details, no crumbs left behind. 👑

This was lastdb 712, from December 2015, and yes, the manual section is LASTDB(1) — say it with your chest. Byeeeee! 💖✨🎀🦋🌸💅🫶

📦 where this page comes from