LAST-SPLIT5(1)

📦
version 1447 · 2 versions
, in debian bookworm

💖 NAME 💖

last-split5 — bestie, this one estimates "split" or "spliced" alignments. That's the whole job. That's the assignment. ✨

🌸 SYNOPSIS 🌸

last-split5-plain [options] LAST-alignments.maf

Like, that's it. Options, then your .maf file. Slay. 💅

🦋 DESCRIPTION 🦋

Okay so here's the vibe: you feed it alignments of query sequences against a genome, and it figures out the genomic source of each part of each query. And the iconic part? Different parts of ONE query are allowed to come from different parts of the genome. It's giving main character energy, it's giving "I contain multitudes," it's giving split reads. Periodt. 👑

✨ OPTIONS ✨

  • -h, --help — show this help message and exit. Your lil emotional support flag. 🫶
  • -f, --format=FMT — output format: MAF, MAF+. Pick your aesthetic. 🎀
  • -r, --reverse — reverse the roles of the 2 sequences in each alignment. Switcheroo. 🔄
  • -g, --genome=NAME — lastdb genome name. Gotta tell it which genome, bestie.
  • -d, --direction=D — RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1). Know which way your RNA is facing, no cap.
  • -c, --cis=PROB — cis-splice probability per base (default: 0.004).
  • -t, --trans=PROB — trans-splice probability per base (default: 1e-05).
  • -M, --mean=MEAN — mean of ln[intron length] (default: 7.0). Yes, natural log. Yes, really. 😭
  • -S, --sdev=SDEV — standard deviation of ln[intron length] (default: 1.7).
  • -m, --mismap=PROB — maximum mismap probability (default: 1.0).
  • -s, --score=INT — minimum alignment score (default: e OR e+t*ln[100]). That formula is not a typo, it is ✨the default✨.
  • -n, --no-split — write original, not split, alignments. Chaos mode: refuse to do the thing. 🙈
  • -b, --bytes=B — maximum memory (default: 8T for split, 8G for spliced). Two different defaults depending on the mode, so watch out. 👀
  • -v, --verbose — be verbose. Talk to me, tell me everything. 🗣️
  • -V, --version — show version information and exit. 💜
Heads up bestie: that -b default changes depending on whether you're doing split (8T) or spliced (8G) — it's not one number for everything. And -s has a whole formula as its default. Read the defaults. Trust. 🌈

That's the whole page, and that's the whole vibe. This lil manual is last-split5 version 1447, and it's dated February 2023. Go split some alignments, you absolute icon. 🧚💖⭐

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