NTCARD(1)

📦 version 1.2.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NTCARD — like, the streaming algorithm bestie 💖

okay so first things first, we're talking about ntcard, and the whole vibe is: a streaming algorithm that estimates cardinality in genomics datasets. that's it, that's the girl. she counts your k-mers without ever holding your whole file in memory, which is lowkey iconic behavior. 🧚

✨ SYNOPSIS ✨

ntCard [OPTION]... FILE(S)...

🌸 DESCRIPTION 🌸

she estimates the k-mer coverage histogram in your FILE(S). like, all of them. every single one. slay. 👑

the files she'll happily eat:

  • fastq
  • fasta
  • sam
  • bam

and compressed formats too, because she's not picky:

  • gz
  • bz2
  • zip
  • xz

also!! if you've got a file that just contains a list of file names, one per row, you can hand it over with an @ prefix. the @ is doing a lot of work there but she gets it. 🫶

🎀 Options 🎀

  • -t, --threads=N — use N parallel threads. default is [1]. and ngl, if your input files are >=2, you should be using N>=2, otherwise what are you even doing bestie 😭
  • -k, --kmer=N — the length of the kmer. that's her whole personality, she's a kmer counter.
  • -g, --gap=N — the length of the gap in the gap seed. default is [0]. now listen: g mod 2 must equal k mod 2 unless g == 0. also, -g does not support multiple k currently — that's just the rules, no cap.
  • -c, --cov=N — the maximum coverage of kmer in the output. default is [1000]. anything past that gets clipped, bye 💅
  • -p, --pref=STRING — the prefix for your output file name(s). choose it wisely, it's giving branding ✨
  • -o, --output=STRING — the name for the output file. use this one when the output should be a single file, i.e. when you're not out here making a whole family of output files.
  • --help — display this help and exit. no thoughts, just help.
  • --version — output version information and exit. she'll tell you who she is 💜

😭 REPORTING BUGS 😭

found a bug? do NOT suffer in silence, that's not the energy. report it to:

https://github.com/bcgsc/ntCard/issues

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. legend behavior, honestly. 🌈

okay and to close it out: this is all about ntcard 1.2.2, dated April 2021. stay hydrated, count your k-mers, and remember — streaming is a lifestyle. 🦋💖

📦 where this page comes from