HILIVE-BUILD(1)

📦 version 2.0a, in debian bookworm, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu stonking

💖 HILIVE-BUILD 💖

okay bestie, listen up — this is hilive-build, a user command living its best life in section 1 of the manual, and it's literally the index creation tool for HiLive — Realtime Alignment of Illumina Reads. that's the whole NAME moment, slay. if you're here it's because you need to build an index before HiLive can do its realtime alignment thing, and honestly? iconic behavior.

✨ SYNOPSIS ✨

hilive-build [options]

that's it. that's the whole vibe. options in, index out. 🦋

🎀 OPTIONS 🎀

GENERAL OPTIONS 💅

these are the "just here to say hi" options. no index gets built, but you get info.

  • -h [ --help ] — prints this help message and then dips. that's it, that's the whole job. ✨
  • -l [ --license ] — prints the licensing information and exits. read it, it's giving legally binding. 📜

REQUIRED OPTIONS 👑

do NOT skip these, i'm so serious. no cap. these are the ones the tool actually needs or it's not happening.

  • -i [ --input ] arg — the reference genome(s), in (multi-)FASTA format. 🧬 [REQUIRED]
  • -o [ --out-prefix ] arg — the output file prefix. several files sharing that same prefix will get created. 📁 [REQUIRED]

OTHER OPTIONS 🌸

the little extra settings, for when you want to be specific about your reference ids.

  • --do-not-convert-spaces — do not convert all spaces in reference ids to underscores. the default is that converting is on, so this flag is you saying "hands off my spaces, bestie." 🙈
  • --trim-after-space — trim all reference ids after the first space. [Default: false] ✂️

🌈 EXAMPLE 🌈

here's what it actually looks like in the wild:

hilive-build --input hg19.fa --out-prefix ./index/hg19

see? reference in, prefix out, index achieved. main character energy fr fr. 🔥

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. ty for your service king 🫶

lowkey a reminder bestie: --input and --out-prefix are REQUIRED. the other two options are optional. don't come crying to me when it yells at you. 😭

and that's the whole page, babes ✨ this was hilive-build version 2.0a, dated October 2019, and yes i read the entire thing so you don't have to. go build that index, you're doing amazing sweetie 💖🎀🦋

📦 where this page comes from