GMER_COUNTER(1)

📦 version 4.0+git20221122.71e6625, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

👑 GMER_COUNTER — bestie's guide to counting k-mers 💅

okay so. welcome to gmer_counter, a little icon from the GenomeTester user manuals (that's the manual name btw, GMER_COUNTER(1) if you're keeping receipts). what does she do? she counts k-mers straight out of raw reads in a FASTQ file. no cap. that's the whole job and she does it gorgeously ✨

✨ SYNOPSIS ✨

gmer_counter [OPTIONS] <SEQUENCES...>

literally just hand her your options and your sequences and she goes to work. main character energy fr fr 🦋

🎀 OPTIONS 🎀

  • -db DATABASE — the SNP/KMER database file. your source of truth, your blueprint, your moment 💖
  • -dbb DBBINARY — binary database file. same vibe, binary form 🧚
  • -w FILENAME — write the binary database out to a file. save it for later bestie 💾
  • -32 — use 32-bit integers for the counts. default is 16-bit, so only reach for this if your numbers are getting big big 🌈
  • --max_kmers NUM — maximum number of kmers per node. cap it 🎀
  • --header — print a header row. yes she's polite 💅
  • --total — print the total number of kmers per node. the whole vibe summed up 🔥
  • --unique — print the number of nonzero kmers per node. only the ones that actually showed up ⭐
  • --kmers — print individual kmer counts. this is the default if you don't ask for any other output, so it's the fallback queen 👑
  • --compile_index — add the read index to the database and write it out to a file. indexing era 📇
  • --distribution NUM — print the kmer distribution, up to the given number. give her a ceiling 🍓
  • --num_threads — number of worker threads. default is 24, because she multitasks like it's nothing 💜
  • --low_memory — optimize for low memory usage. for when your RAM is on a budget 😭
  • -D — increase the debug level. stack it if you're nosy 🙈

🌸 EXAMPLES 🌸

you could find some usage examples in:

/usr/share/doc/genometester/README.FastGT.md

go read it, it's giving tutorial 🫶

🔥 SEE ALSO 🔥

the whole friend group, we love a supportive squad 💖

GenomeTester — version dated 31 May 2018, manual page GMER_COUNTER(1). that's the sign-off bestie, go count some kmers, ily, bye 💅✨🦋

📦 where this page comes from