IDBA_TRAN(1)

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

✨ IDBA_TRAN ✨

okay bestie, gather round, because idba_tran is literally the Iterative de Bruijn Graph Assembler for next-generation transcriptome sequencing data 💖 and it is so much cooler than it sounds. this is the manual page for it. yes it's a manual page. yes it's giving main character energy. let's go 🦋

🌸 SYNOPSIS 🌸

idba_tran -r read.fa -o output_dir

that's it. that's the whole vibe. give it reads, give it a place to put the output, and it does its little iterative de Bruijn thing ✨

💅 DESCRIPTION 💅

IDBA-Tran — the Iterative de Bruijn Graph Assembler for next-generation transcriptome sequencing data. periodt. that's the whole job description and honestly? iconic.

🎀 Allowed Options: 🎀

here's the full menu, no skips, no "you get the gist" — every single flag, every single default, all of it 🫶

  • -o, --out arg (=out) — the output directory. where all the goods go 📁
  • -r, --read arg — fasta read file (<=128) 🧬
  • -l, --long_read arg — fasta long read file (>128) 🌈
  • --mink arg (=20) — minimum k value (<=124)
  • --maxk arg (=60) — maximum k value (<=124)
  • --step arg (=10) — 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 (yes, "supoort". we keep it exactly as written, no notes 💀)
  • --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_transcript arg (=300) — minimum size of transcript
  • --similar arg (=0.95) — similarity for alignment
  • --max_mismatch arg (=3) — max mismatch of error correction
  • --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
  • --max_isoforms arg (=3) — maximum number of isoforms
  • --max_component_size arg (=30) — maximum size of components
ngl, if a flag says do not do something, that's the whole point — don't be surprised when the thing doesn't happen 🙈

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, absolute legend, we love a manpage author who shows up for the people 💜

and that's a wrap on the idba_tran page, bestie ✨ this one's idba_tran 1.1.3, dated March 2020 — yeah, it's been slaying since 2020 and it's still the moment. byeee 🎀🦋💖

📦 where this page comes from