IDBA(1)

📦 version 1.1.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 IDBA(1) — Iterative de Bruijn Graph Assembler 💖

User Commands vibes only. ✨

🌸 NAME 🌸

idba — Iterative de Bruijn Graph Assembler ✨

🦋 SYNOPSIS 🦋

idba_ud -r read.fa -o output_dir

👑 DESCRIPTION 👑

IDBA- Iterative de Bruijn Graph Assembler. That's the name, bestie, and that's the whole energy. Iterative, de Bruijn, Graph, Assembler — iconic. 🧬✨

🎀 Allowed Options: 🎀

  • -o, --out arg (=out) — output directory. Where the magic lands. 💾
  • -r, --read arg — fasta read file (<=128). Keep it under or equal to 128, bestie. 🌸
  • --read_level_2 arg — paired-end reads fasta for second level scaffolds. Level 2 unlocked. 🔓
  • --read_level_3 arg — paired-end reads fasta for third level scaffolds. Level 3, let's go. 🦋
  • --read_level_4 arg — paired-end reads fasta for fourth level scaffolds. Level 4 vibes. 🌿
  • --read_level_5 arg — paired-end reads fasta for fifth level scaffolds. Level 5, final level energy. 🍑
  • -l, --long_read arg — fasta long read file (>128). Long reads only, periodt. 📏
  • --mink arg (=20) — minimum k value (<=124). Floor k, no lower. ⬇️
  • --maxk arg (=50) — maximum k value (<=124). Ceiling k, no higher. ⬆️
  • --step arg (=10) — increment of k-mer of each iteration. Step by step, iteration by iteration. 👟
  • --prefix arg (=3) — prefix length used to build sub k-mer table. Prefix tea. 🫖
  • --min_count arg (=2) — minimum multiplicity for filtering k-mer when building the graph. Filter those k-mers. 🧹
  • --min_support arg (=1) — minimum supoort in each iteration. Yes, "supoort" — that's the manpage spelling, bestie. 😭
  • --num_threads arg (=0) — number of threads. Parallelize, slay. 🧵
  • --seed_kmer arg (=30) — seed kmer size for alignment. Seed it. 🌱
  • --min_contig arg (=200) — minimum size of contig. No tiny contigs allowed. 🚫
  • --similar arg (=0.95) — similarity for alignment. Similarity threshold, locked in. 🔒
  • --max_mismatch arg (=3) — max mismatch of error correction. Mismatch limit. ⚠️
  • --min_pairs arg (=3) — minimum number of pairs. Pairs minimum. 👯
  • --no_coverage — do not iterate on coverage. No coverage iteration. 🚫
  • --no_correct — do not do correction. No correction, periodt. 🙅
  • --pre_correction — perform pre-correction before assembly. Pre-correct before assembly. ✅

💜 AUTHOR 💜

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

💖 That's the tea: idba 1.1.3, March 2020, IDBA(1). Stay assembling, bestie. 🫶✨
📦 where this page comes from