SUBREAD-BUILDINDEX(1)

📦
version 2.0.8 · 2 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ SUBREAD-BUILDINDEX ✨

okay bestie, so this is subread-buildindex, part of the subread family — a whole toolkit for processing next-gen sequencing data 🧬 and this particular little icon is the one that builds your index. index-building is like laying out your closet before you get dressed, it's not the glamorous part but everything after it slays 💅

🎀 NAME 🎀

subread-buildindex — toolkit for processing next-gen sequencing data

🌸 DESCRIPTION 🌸

so first things first, we're on Version 2.0.4 ⭐

Here's how you actually call it:

./subread-buildindex [options] -o <basename> {FASTA[.gz] file1}\

[FASTA[.gz] file2] ...

(yes that backslash is literally part of it, don't come for me 🙈)

💖 Required arguments 💖

these are not optional, bestie, you HAVE to bring them:

  • -o <basename> — the base name of the index that's gonna get created. this is the name you're birthing into the world, choose it with care 👑

✨ Optional arguments ✨

now for the fun part, the little knobs and dials:

  • -F — build a full index for the reference genome. 16bp subreads get extracted from every single position of the reference genome. heads up though: the size of the index is typically 3 times the size of the index you'd get from using the default setting. it's giving "go big or go home" 🔥
  • -B — create one block of index. the built index won't get split into multiple pieces. this means the largest amount of memory will be requested when you're running alignments, but it enables the maximum mapping speed to be achieved. also important: this option overrides -M when it's provided as well. so if you pass both, -B is the main character and -M is just standing there 😭
  • -M <int> — size of requested memory (RAM) in megabytes, 8000 by default.
  • -f <int> — specify the threshold for removing uninformative subreads (aka those highly repetitive 16mers in the reference). 100 by default.
  • -c — build a color-space index. 🌈
  • -v — output the version of the program.
For more information about these arguments, please refer to the User Manual. 📖 (fr fr, go read it)

💜 AUTHOR 💜

This manpage was written by Alexandre Mestiashvili for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole page, bestie!! this was subread-buildindex 2.0.3, dated March 2023 — go build some iconic indexes, no cap 💖✨🎀

📦 where this page comes from