DISTANCEEST(1)

📦
version 2.3.10 · 6 versions
, in ubuntu resolute, ubuntu stonking

💖 DISTANCEEST 💖

okay so bestie, welcome to DistanceEst — a lil tool that estimates distances between contigs using paired-end alignments 🧚✨ it's giving "I know where you live and how far apart you are" fr fr

It lives in the User Commands section of the manual, and honestly? she's iconic for it 💅

🌸 NAME 🌸

DistanceEst — Estimate distances between contigs using paired-end alignments. 🦋

✨ SYNOPSIS ✨

DistanceEst -k<kmer> -s<seed-length> -n<npairs> [OPTION]... HIST [PAIR]

Like, that's the whole vibe. Give her a histogram, maybe give her some pairs, and she'll do the math 💖

🫶 DESCRIPTION 🫶

Estimate distances between contigs using paired-end alignments. That's the whole mission statement, periodt. 👑

🌈 Arguments

  • HIST — the distribution of fragments size 📊
  • PAIR — alignments between contigs 🧬

🎀 Options

  • --mind=N — minimum distance between contigs, and the default is -(k-1) ✨
  • --maxd=N — maximum distance between contigs 🚧
  • --fr — force the orientation to forward-reverse ➡️⬅️
  • --rf — force the orientation to reverse-forward ⬅️➡️
  • -k, --kmer=N — sets --mind to -(k-1) bp 🔢
  • -l, --min-align=N — the minimal alignment size, default 1 📏
  • -n, --npairs=NPAIRS — minimum number of pairs 🧮
  • -s, --seed-length=L — minimum length of the seed contigs 🌱
  • -q, --min-mapq=N — ignore alignments with mapping quality less than this threshold, default 10 🙈
  • -o, --out=FILE — write result to FILE 📝
  • --mle — use the MLE (default) (maximum likelihood estimator) 🏆
  • --median — use the difference of the population median and the sample median 📉
  • --mean — use the difference of the population mean and the sample mean 📈
  • --dist — output the graph in dist format (default) 📦
  • --dot — output the graph in GraphViz format 🎨
  • --gv — output the graph in GraphViz format 🎨
  • --gfa — output the graph in GFA2 format 🧬
  • --gfa2 — output the graph in GFA2 format 🧬
  • -j, --threads=N — use N parallel threads, default 1 🧵
  • -v, --verbose — display verbose output 🗣️
  • --help — display this help and exit 🆘
  • --version — output version information and exit 🏷️
  • --db=FILE — specify path of database repository in FILE 🗄️
  • --library=NAME — specify library NAME for sqlite 📚
  • --strain=NAME — specify strain NAME for sqlite 🦠
  • --species=NAME — specify species NAME for sqlite 🐾

💜 AUTHOR 💜

Written by Jared Simpson and Shaun Jackman. legends, honestly 🫶

😭 REPORTING BUGS 😭

Report bugs to <abyss-users@bcgsc.ca>. no cap, they wanna hear about it, don't be shy 📬

Copyright 2014 Canada's Michael Smith Genome Sciences Centre 🌸

okay so that's a wrap bestie 💖 this page is from ABySS 2.3.10, dated January 2026 — so like, fresh off the press, main character energy fr fr. slay, go estimate some distances ✨🎀💅

📦 where this page comes from