GAP4(1)

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

💖 GAP4(1) — the gap4 girlies' era 💖

User Commands · Genome Assembly Program, part of the staden package · manual page, but make it a group chat 🫶

✨ NAME ✨

gap4 — Genome Assembly Program (she's part of the staden package, bestie 💅)

🌸 SYNOPSIS 🌸

gap4 [-ro] [-maxseq <number>] [-maxdb <number>] [-skip_notes]
[DATABASE_NAME.V]

Yeah she takes args, and yeah the last one is literally your database's name with a .V on the end. iykyk 💜

🦋 DESCRIPTION 🦋

Okay so. gap4 is a Genome Assembly Program. Like, the Genome Assembly Program. She's got every tool you'd ever expect an assembly program to have, plus a whole bunch of unique features nobody else has, plus an interface that is genuinely so easy to use it's giving ✨main character energy✨.

The og version got written up in Bonfield,J.K., Smith,K.F. and Staden,R. A new DNA sequence assembly program. Nucleic Acids Res. 24, 4992-4999 (1995) — yes that's a real citation, no I'm not skipping it, academic integrity is iconic 📚💅

gap4 is very big and powerful. Like, huge. Everybody ends up using just a subset of the options and has their own fave little way of getting around and doing stuff. And yes, there is a lot of it, but bestie, you're genuinely encouraged to read through the whole documentation at least once — just to find out what's even possible and figure out which way suits your own work best 🧚

At the very least, read the whole of this introductory chapter. In the long run it will save you time, fr fr ⏳

💅 OPTIONS 💅

  • -ro — read-only mode. 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 when the DB opens
  • -(no_)exec_notes — (do not) execute OPEN/CLOS notes when the database opens
  • -(no_)rawdata_note — (do not) use the RAWD note instead of the RAWDATA env. variable
  • -(no_)csel — (do not) start up the contig selector when the db opens
  • -display — the X Display to use 🖥️
  • -bitsize N — specifies the aux file bitsize for new databases (32/64)
  • -sync — use synchronous mode for the display server (this one's for debugging 👀)
  • -- — end of argument list, that's a wrap periodt 🎀

🔥 SEE ALSO 🔥

http://staden.sourceforge.net/manual/gap4_unix_2.html — go read it, she ate 💖

okay and that's the whole page bestie, we did it 🌈 this one's from gap4 2.0.0+b10, dated April 2014 — vintage but still serving 👑 byeeee 🦋✨

📦 where this page comes from