SURANKCO-SCORE(1)

📦 version 0.0.r5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SURANKCO-SCORE 💖

okay bestie, so you know how surankco-score is a User Commands page? yeah. it lives in section 1 of the manual and honestly it's giving main character energy. let's get into it 🫶

✨ NAME ✨

surankco-score — alignment of contigs and reference genomes and score calculation

like, it lines up your contigs with your reference genomes and then it scores the whole thing. icon. 💅

🌸 SYNOPSIS 🌸

surankco-score [options]

just the one line, no positional drama, all the vibes live in the options 💖

🦋 DESCRIPTION 🦋

Alignment of contigs (FASTA format) and reference genomes (FASTA format) and score calculation

that's it, that's the whole thing — you feed it contigs in FASTA, you feed it reference genomes in FASTA, it aligns them, it calculates scores. no cap, it's that simple 🔥

🎀 OPTIONS 🎀

  • -a ASSEMBLIES, --assemblies=ASSEMBLIES — hand over a whole list of assembly files, comma separated 💫 heads up though: the correct suffixes are mandatory here, like the dress code is enforced. default is "*.contigs.fasta"
  • -d DIRECTORY, --directory=DIRECTORY — point it at a directory that's full of assembly files in the indicated format (e.g. "*.contigs.fasta"). it'll go shopping in there itself 🛍️
  • -f ASSEMBLY.SUFFIX, --assembly.suffix=ASSEMBLY.SUFFIX — tell it the assembly format/suffix you're working with. default is "contigs.fasta" ✨
  • -r REFERENCE.SUFFIX, --reference.suffix=REFERENCE.SUFFIX — same deal but for the reference format/suffix. default is "ref.fasta" 💜
  • -p PDF.HISTOGRAMS, --pdf.histograms=PDF.HISTOGRAMS — pick a name for the score histogram pdf, because obviously you need a little picture of your results. default is "surankco_score_histograms.pdf" 📊
  • -m MEMORY, --memory=MEMORY — sets the maximum memory usage (in Gb) of Java's virtual machine. default is 32. and bestie, listen: if your big data sets start reporting heap space problems, try to increase this. the JVM is hungry and she will tell you 😭
  • -h, --help — show this help message and exit. the classic. the beloved. the "I forgot what -f does again" emergency exit 🚪

👑 AUTHOR 👑

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

respect where respect is due, fr fr 🌈

also quick vibe check: surankco-score 0.0.r5 from March 2016 — that's the version and the date, so if you're citing it, that's the receipt 🧾✨

and that's the whole page, bestie. go align something and slay 💅💖🌸

📦 where this page comes from