IVA_QC_MAKE_DB(1)

📦
version 1.0.11 · 6 versions
, in debian trixie, ubuntu questing

✨ NAME ✨

iva_qc_make_db — bestie, this is the lil tool that makes a database as input for iva_qc 💖

🌸 SYNOPSIS 🌸

usage: iva_qc_make_db [options] <output directory>

🦋 DESCRIPTION 🦋

okay so real talk: you wanna run iva_qc but it needs a database to eat first, right? that's literally this program. you point it at an output directory and it goes and builds you the goods. no cap. 🫶

🎀 positional arguments:

  • Directory_name — the name of the output directory. that's where everything lands, queen. 👑

💅 options:

  • -h, --help — show this help message and exit. classic. the "help me bestie" button. ✨
  • --add_to_ref Filename — filename of Genbank IDs or GI numbers to be added to the database. the format is: a whitespace separated list of GI numbers on each line. one line defines one genome — like, for real, flu has 8 segments, so you put 8 GI numbers on one line for one flu reference. one line = one genome, don't mix it up fr fr. 🧬
  • --skip_viruses — do not run kraken-build --download-library viruses when building the database. sounds chill but listen: if you use this option, then --add_to_ref must also be used. no --add_to_ref, no deal. 😤
  • --threads INT — number of threads to use [1]. crank it up if you got the cores, main character energy. 🔥
  • --minimizer_len INT — the number to pass to the kraken-build minimizer_len option [13]. you don't gotta touch this unless you know why you're touching it. 🙈
  • --max_db_size INT — the number to pass to the kraken-build max_db_size option [3]. again, defaults are there for a reason. 💀
  • --verbose — be verbose. be loud. be the main character of your terminal. 💅
  • --version — show program's version number and exit. the classic "who even am I" flag. ⭐
heads up bestie: --skip_viruses and --add_to_ref are a package deal. skip the viruses and you must hand over your own references, periodt.

🌈 SEE ALSO 🌈

ok so like... the original page doesn't list any other pages here, so we're keeping it exactly as it is — nothing to add, nothing to skip. iykyk. 🎀

that's the whole vibe, babe — go build that database 💜

iva_qc_make_db 1.0.8 · December 2024 · from the User Commands section (man page IVA_QC_MAKE_DB(1)) 🦋✨

📦 where this page comes from