LAST-SPLIT(1)

💖 LAST-SPLIT(1) — User Commands 💖

okay bestie, sit down, hydrate, and let me tell you about last-split, a lil last-split(1) era icon from the User Commands corner of your manual pages. she's giving "estimates split or spliced alignments" and honestly? she ate. ✨

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🌸 NAME 🌸

last-split — estimates "split" or "spliced" alignments. no cap, that's the whole job description. 🫶

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🦋 SYNOPSIS 🦋

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

that's it. that's the summoning ritual. one input file, a pile of [options], and vibes. 💅

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✨ DESCRIPTION ✨

So here's the tea. 🍓 last-split reads your alignments of query sequences to a genome — that's the input, hi — and then it estimates the genomic source of each part of each query.

The iconic part? It lets different parts of ONE query come from DIFFERENT parts of the genome. bestie that's not a bug that's the whole main character energy of it. one query, many homes. 💀

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👑 OPTIONS 👑

Every single flag, accounted for, no girls left behind:

• -h, --help — shows this help message and then dips. polite. 🎀
• -f, --format=FMT — your output format, girl. the options are MAF, MAF+.
• -r, --reverse — flips the roles of the 2 sequences in each alignment. they switch places, it's giving Freaky Friday.
• -g, --genome=NAME — the lastdb genome name. you gotta tell her whose genome we're talking about. 🧬
• -d, --direction=D — RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1). pick your lane, or don't, 2 says "why not both" 💅
• -c, --cis=PROB — cis-splice probability per base (default: 0.004). tiny number, big consequences.
• -t, --trans=PROB — trans-splice probability per base (default: 1e-05). even tinier. she's shy. 🙈
• -M, --mean=MEAN — mean of ln[intron length] (default: 7.0). yes we live in log space, we're that kind of girl.
• -S, --sdev=SDEV — standard deviation of ln[intron length] (default: 1.7). spread it out, slay. 🌈
• -m, --mismap=PROB — maximum mismap probability (default: 1.0). emphasis on maximum, not minimum. read it twice.
• -s, --score=INT — minimum alignment score (default: e OR e+t*ln[100]). that default is literally a whole little formula, copy it exactly, don't come for me. ⭐
• -n, --no-split — writes the original, not split, alignments. the "no thoughts, just original" setting. 💜
• -b, --bytes=B — maximum memory (default: 8T for split, 8G for spliced). yes that's terabytes vs. gigabytes, they are NOT the same bestie, do not confuse them. 😭
• -v, --verbose — be verbose. she will yap. you asked for it. 🗣️
• -V, --version — show version information and then exit. bye! 👋

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ok real talk for one sec: the memory default is 8T for split and 8G for spliced — that's a 1000x difference, so check which mode you're in before you go allocating. not me warning you twice 💀

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and that's the whole page, bestie. last-split 💖, from page 1654, dated August 2026 — she's a little legend and now she's your little legend. go estimate some alignments. periodt. 🫶✨🎀