SGA-ALIGN(1)

📦 version 0.10.15, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu stonking

✨ SGA-ALIGN — the manual page, but make it cute ✨

okay so bestie, you've wandered into the sga-align manpage, which lives in the User Commands section of the manual. Pull up a chair, grab a strawberry 🍓, and let's get you aligned. literally.

💖 NAME 💖

sga-aligm — align reads to contigs 🧬

(no babe, that's not a typo I made, the page fr says sga-aligm, we're keeping it, it's iconic, we don't edit the queen 💅)

🌸 SYNOPSIS 🌸

sga-align [options] <contigs file> <input files>

so you give it some options, a contigs file, and your input files, and it goes to work. that's the whole vibe. ✨

🦋 DESCRIPTION 🦋

okay so here's the major goal of SGA, and it's a good one: it wants to be very memory efficient. not just kinda efficient. very. and the way it pulls that off is by using a compressed representation of DNA sequence reads. so your RAM can breathe. 🫶

SGA is a de novo assembler for DNA sequence reads. it's built on Gene Myers' string graph formulation of assembly, and it uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. no cap, that's the actual architecture. 🔥

👑 OPTIONS 👑

here's where the actual knobs live. there are two. that's it. two options. we love a minimal queen. ✨

  • --name=STR — use STR as the basename for the output files. so like, whatever you name it, that's what your output files are gonna be called. pick something cute. 🎀
  • -t,--threads=N — use N threads when running bwa. more threads, more speed, as long as your machine can handle the main character energy. ⭐

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. 🫶 thank you Andreas, we appreciate you.

heads up bestie: that's genuinely every option on this page — --name=STR and -t,--threads=N. don't go looking for more, there aren't more. 🙈

and that's the whole thing! this page is from sga-align 0.10.15, dated September 2016 🦋 — so yes, it's a little vintage, but vintage is a vibe. go align something. slay. 💅✨🌸

📦 where this page comes from