GAP4(1)

📦 version 2.0.0+b11, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 GAP4(1) — User Commands, bestie edition 💖

okay so real talk: the page is officially filed under GAP4(1) in the User Commands corner of your man pages, and it's here to introduce you to gap5. yes, the naming is a little chaotic. we love that for it. 🎀

✨ NAME ✨

gap5 — Genome Assembly Program (part of staden package)

🌸 SYNOPSIS 🌸

gap5 [-ro] [-maxseq <number>] [-maxdb <number>] [-skip_notes]
[DATABASE_NAME.V]

🦋 DESCRIPTION 🦋

Gap5 is a Genome Assembly Program, and no bc it does not play. It's got every tool you'd expect an assembly program to have, plus a bunch of unique features and a genuinely very easily used interface. The original version got a whole writeup — that's Bonfield,J.K., Smith,K.F. and Staden,R. A new DNA sequence assembly program. Nucleic Acids Res. 24, 4992-4999 (1995), iykyk 📚✨

ngl, Gap5 is very big and powerful. Everybody uses some subset of the options and has their own fave way of getting around. And like… yes, there is a LOT. But bestie, the docs are literally begging you to read the whole thing once — just once!! — so you can find out what's even possible and which workflow fits your vibe best. At the very least, read all of this introductory chapter, because in the long run it will save you time. periodt. ⏳💅

👑 OPTIONS 👑

  • -ro — Read-only. Look, don't touch. 🙈
  • -maxseq N — Initial maximum total consensus length
  • -maxdb N — Initial maximum number of contigs + readings
  • -(no_)check — (Do not) run Check Database upon DB open
  • -(no_)exec_notes — (Do not) execute OPEN/CLOS notes upon database open
  • -(no_)rawdata_note — (Do not) use RAWD note instead of RAWDATA env. variable
  • -(no_)csel — (Do not) start up the contig selector upon db open
  • -display — X Display to use
  • -bitsize N — Specifies the aux file bitsize for new databases (32/64)
  • -sync — Use synchronous mode for display server (debugging)
  • -- — End of argument list
heads up bestie: -skip_notes shows up in the synopsis but not in the options list, so don't come for me, I'm just reporting what the page says 🫶

okay that's the whole thing!! this page is from gap5 2.0.0+b10, dated April 2014, and it lives under the GAP4(1) name. slay, go assemble something iconic 🧚💜

📦 where this page comes from