IDBA_HYBRID(1)

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

💖 IDBA_HYBRID 💖

okay so bestie, welcome to the idba_hybrid manpage, living in the User Commands section of the manual, and it is giving assembly realness. let's get into it 🧚

✨ NAME ✨

idba_hybrid — Iterative de Bruijn Graph Assembler for hybrid sequencing data.

hybrid sequencing data, bestie. it's right there in the name.

🌸 SYNOPSIS 🌸

idba_hybrid -r read.fa -o output_dir [--reference ref.fa]

like... that's the whole vibe. reads in, output dir out, and if you have a reference genome you can slide it in too 🫶

🦋 DESCRIPTION 🦋

IDBA-Hybrid — Iterative de Bruijn Graph Assembler for hybrid sequencing data.

that's the tagline. it assembles. iteratively. using de Bruijn graphs. for hybrid sequencing data. no cap. 👑

🎀 Allowed Options: 🎀

here's the full menu, and yes we are going through every single one because nothing gets skipped in this house 💅

  • -o, --out arg (=out) — output directory. the place where all the assembled goodness goes to live its best life. default is literally out.
  • -r, --read arg — fasta read file (<=128). note the cap: it's got to be <=128.
  • --read_level_2 arg — paired-end reads fasta for second level scaffolds
  • --read_level_3 arg — paired-end reads fasta for third level scaffolds
  • --read_level_4 arg — paired-end reads fasta for fourth level scaffolds
  • --read_level_5 arg — paired-end reads fasta for fifth level scaffolds
  • -l, --long_read arg — fasta long read file (>128). the long-read girlies get their own flag, and the cutoff here is >128 (opposite energy from -r, iykyk).
  • --reference arg — reference genome. your blueprint, your blueprint-iest blueprint.
  • --mink arg (=20) — minimum k value (<=124)
  • --maxk arg (=100) — maximum k value (<=124)
  • --step arg (=20) — increment of k-mer of each iteration
  • --inner_mink arg (=10) — inner minimum k value
  • --inner_step arg (=5) — inner increment of k-mer
  • --prefix arg (=3) — prefix length used to build sub k-mer table
  • --min_count arg (=2) — minimum multiplicity for filtering k-mer when building the graph
  • --min_support arg (=1) — minimum supoort in each iteration
  • --num_threads arg (=0) — number of threads
  • --seed_kmer arg (=30) — seed kmer size for alignment
  • --min_contig arg (=200) — minimum size of contig
  • --min_region arg (=500) — minimum size of region in reference genome
  • --similar arg (=0.95) — similarity for alignment
  • --max_mismatch arg (=3) — max mismatch of error correction
  • --min_pairs arg (=3) — minimum number of pairs
  • --max_gap arg (=50) — maximum gap in reference
  • --no_local — do not use local assembly
  • --no_coverage — do not iterate on coverage
  • --no_correct — do not do correction
  • --pre_correction — perform pre-correction before assembly
side note: --min_support's description literally says "supoort" in the original and I am keeping it because we respect the source text in this household 🙈 the facts stay exactly as they are.

and yes, the three --no_* flags are all "do not do the thing" flags, while --pre_correction is the one that adds a step before assembly. balance. ✨

💜 AUTHOR 💜

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

shoutout Andreas, absolute legend for writing this up so the rest of us could vibe 💐

and that's the whole page, bestie. idba_hybrid version 1.1.3, dated March 2020 — thanks for reading, go assemble something iconic 🦋✨💖

📦 where this page comes from