CONTIGOVERLAPS(1)

📦 version 2.18, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 CONTIGOVERLAPS 💖

okay bestie, welcome to the manual page for contigOverlaps — that's section 1 of the manual btw, so you know it's a user command. and yes, the full title it goes by is CONTIGOVERLAPS(1) 🦋

✨ NAME ✨

contigOverlaps — it's giving ContigOverlaps nosha. that's the whole vibe. 🎀

🌸 SYNOPSIS 🌸

so here's the shape of it, copy it exactly okay:

contigOverlaps <options> firstAssemblyBams.fofn secondAssemblyBams.fofn
[ ... ]

you hand it a first assembly BAMs file (firstAssemblyBams.fofn), then a second one (secondAssemblyBams.fofn), and then, like, more if you want — the [ ... ] is literally right there saying there can be extra stuff after. slay. 💅

💜 OPTIONS 💜

  • --help — prints out this message. that's it. that's the whole job. main character behaviour fr. ✨
  • --percentIdentity — takes an arg, and it's the minimum end-to-end % identity that a read needs to qualify. the default is 97. so if you don't say anything, it's 97, no cap. 🔥

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. iconic of them honestly 🫶

okay and that's the whole page bestie, no notes 💖 the version is contigOverlaps 2.15 and it's dated May 2020 — so yeah, a lil vintage, but we love her. periodt. 🎀✨💜

📦 where this page comes from