CENTRIFUGE-DOWNLOAD(1)

✨ NAME ✨

centrifuge-download — the centrifuge helper bestie that goes and fetches databases for you, no cap 🫶

💫 DESCRIPTION 💫

centrifuge-download [<options>] <database>

Okay so the vibe is simple: you give it a database name, it goes and gets the files. Periodt. 🎀

🌸 ARGUMENT 🌸

• <database> — literally just pick one of refseq, genbank, contaminants or taxonomy, bestie:
  • use refseq or genbank for genomic sequences,
  • contaminants gets contaminant sequences from UniVec and EmVec,
  • taxonomy for taxonomy mappings.

🧚 COMMON OPTIONS 🧚

• -o <directory> — the folder the files get downloaded into. Default: . (yes, the one you're standing in, it's giving home 🏠).
• -P <# of threads> — how many processes to use while downloading (it uses xargs under the hood, slay). Default: 1.

👑 WHEN USING database refseq OR genbank: 👑

• -d <domain> — which domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated, okay? commas are the love language here 💖).
• -a <assembly level> — only download genomes with the specified assembly level. Default: Complete Genome. Use Any for, you guessed it, any assembly level. ✨
• -c <refseq category> — only download genomes in the specified refseq category. Default: any.
• -t <taxids> — only download the specified taxonomy IDs, comma separated. Default: any.
• -r — download RNA sequences, too. Like, why not, treat yourself 🦋.
• -u — filter unplaced sequences.
• -m — mask low-complexity regions using dustmasker. Default: off.
• -l — modify the header to include the taxonomy ID. Default: off.
• -g — download GI map.

💀 Heads up bestie: -m, -l and a whole bunch of these are off by default, so if you wanted them, you have to actually ask. No mind-reading, fr fr.

🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. Iconic of him honestly 💅.

And that's the whole page, bestie!! 🎀 This one's centrifuge-download version 1.0.3, dated October 2021 — go download something gorgeous with it. Mwah. 💖🌸🦋